ClinVar Genomic variation as it relates to human health
NM_000383.4(AIRE):c.967_979del (p.Leu323fs)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000383.4(AIRE):c.967_979del (p.Leu323fs)
Variation ID: 3309 Accession: VCV000003309.60
- Type and length
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Deletion, 13 bp
- Location
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Cytogenetic: 21q22.3 21: 45711063-45711075 (GRCh37) [ NCBI UCSC ] 21: 44291180-44291192 (GRCh38) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Oct 20, 2024 Mar 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000383.4:c.967_979del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000374.1:p.Leu323fs frameshift NM_000383.4:c.967_979delCTGTCCCCTCCGC MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NC_000021.9:g.44291182_44291194del NC_000021.8:g.45711065_45711077del NG_009556.1:g.10303_10315del LRG_18:g.10303_10315del LRG_18t1:c.967_979del - Protein change
- L323fs
- Other names
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- Canonical SPDI
- NC_000021.9:44291179:GCCTGTCCCCTCCGC:GC
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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AIRE | - | - |
GRCh38 GRCh37 |
1134 | 1275 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (1) |
no assertion criteria provided
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Nov 1, 2009 | RCV000003473.7 | |
Pathogenic/Likely pathogenic (15) |
criteria provided, multiple submitters, no conflicts
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Jan 31, 2024 | RCV000049635.45 | |
Pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Mar 1, 2024 | RCV000284330.30 | |
AIRE-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jul 17, 2024 | RCV003407265.5 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Sep 21, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000232541.5
First in ClinVar: Jun 28, 2015 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Pathogenic
(Mar 05, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: unknown
Allele origin:
germline
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Blueprint Genetics
Accession: SCV000927566.1
First in ClinVar: Jul 24, 2019 Last updated: Jul 24, 2019
Comment:
Patient analyzed with Primary Immunodeficiency Panel
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Pathogenic
(Dec 17, 2019)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV001193892.2
First in ClinVar: Apr 06, 2020 Last updated: Jul 04, 2020 |
Comment:
NM_000383.3(AIRE):c.967_979del13(L323Sfs*51) is classified as pathogenic in the context of autoimmune polyglandular syndrome type 1. Sources cited for classification include the following: PMID 17220063, 12050215, 17118990, … (more)
NM_000383.3(AIRE):c.967_979del13(L323Sfs*51) is classified as pathogenic in the context of autoimmune polyglandular syndrome type 1. Sources cited for classification include the following: PMID 17220063, 12050215, 17118990, 9921903, 9837820, 21295522, 17118990 and 12050215. Classification of NM_000383.3(AIRE):c.967_979del13(L323Sfs*51) is based on the following criteria: The variant causes a premature termination codon that is expected to be targeted by nonsense-mediated mRNA decay and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening. (less)
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Pathogenic
(Dec 24, 2020)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696656.3
First in ClinVar: Jan 06, 2018 Last updated: Jan 05, 2021 |
Comment:
Variant summary: AIRE c.967_979del13 (p.Leu323SerfsX51) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Variant summary: AIRE c.967_979del13 (p.Leu323SerfsX51) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 0.00051 in 243022 control chromosomes. c.967_979del13 has been widely reported in the literature as a frequent mutation in multiple individuals affected with Autoimmune Polyglandular Syndrome Type 1 (example, Wang_1998, Dominguez_2006). These data indicate that the variant is very likely to be associated with disease. A mice model of this 13-bp deletion displaying a mild autoimmune phenotype characterized by a disturbance of medullary epithelial compartment, increased levels of activated T cells and autoantibodies against multiple organs has been reported (Hubert_2009). Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Sep 29, 2020)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004175444.1
First in ClinVar: Dec 17, 2023 Last updated: Dec 17, 2023 |
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Pathogenic
(Nov 02, 2023)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002024173.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000629960.9
First in ClinVar: Dec 26, 2017 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Leu323Serfs*51) in the AIRE gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Leu323Serfs*51) in the AIRE gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AIRE are known to be pathogenic (PMID: 11524731, 26141571). This variant is present in population databases (rs779937061, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individual(s) with autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) and is the most common variant found in affected individuals of British or Anglo-American ancestry (PMID: 9837820, 11524731, 27588307). It has also been observed to segregate with disease in related individuals. This variant is also known as c.964del13, c.967_979del13, p.C322del13, or c.1094_1106del. ClinVar contains an entry for this variant (Variation ID: 3309). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Dec 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV001365629.2
First in ClinVar: Jul 04, 2020 Last updated: Apr 20, 2024 |
Comment:
The p.Leu323SerfsX51 variant in AIRE is a well-established pathogenic variant, which represents the most common variant identified in Anglo-American autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) patients (Heino … (more)
The p.Leu323SerfsX51 variant in AIRE is a well-established pathogenic variant, which represents the most common variant identified in Anglo-American autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) patients (Heino 2001 PMID: 11524731, Ferre 2016 PMID: 27588307). It has also been identified in 0.096% (121/125552) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). However, this frequency is low enough to be consistent with a recessive carrier frequency. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 323 and leads to a premature termination codon 51 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the AIRE gene is an established disease mechanism in autosomal recessive APECED. Finally, the p.Leu323SerfsX51 has been reported as Pathogenic by multiple clinical labs in ClinVar (Variation ID 3309). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive APECED. ACMG/AMP Criteria applied: ACMG/AMP criteria applied: PVS1, PM3_VeryStrong. (less)
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Pathogenic
(Mar 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV002585907.15
First in ClinVar: Oct 22, 2022 Last updated: Oct 20, 2024 |
Comment:
AIRE: PM3:Strong, PVS1:Strong, PM2:Supporting, PS3:Supporting
Number of individuals with the variant: 5
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Pathogenic
(Mar 27, 2018)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Athena Diagnostics
Accession: SCV000840734.1
First in ClinVar: Jan 07, 2017 Last updated: Jan 07, 2017 |
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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: yes
Allele origin:
germline
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Genomics England Pilot Project, Genomics England
Accession: SCV001760477.1
First in ClinVar: Jul 27, 2021 Last updated: Jul 27, 2021 |
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Pathogenic
(Feb 14, 2022)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: yes
Allele origin:
germline
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DASA
Accession: SCV002097301.1
First in ClinVar: Feb 20, 2022 Last updated: Feb 20, 2022 |
Comment:
The c.967_979del;p.(Leu323Serfs*51) is a null frameshift variant in the AIRE gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevant … (more)
The c.967_979del;p.(Leu323Serfs*51) is a null frameshift variant in the AIRE gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevant exon to the transcript -PVS1_strong. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 3309; PMID: 11524731; 9837820; 27588307) - PS4. The variant is present at low allele frequencies population databases (rs386833675 - gnomAD 0.0005850%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Leu323Serfs*51) was detected in trans with a pathogenic variant (PMID: 11524731; 9837820; 27588307) - PM3. In summary, the currently available evidence indicates that the variant is pathogenic. (less)
Number of individuals with the variant: 1
Sex: male
Geographic origin: Brazil
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Pathogenic
(May 22, 2022)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
Affected status: yes
Allele origin:
germline
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3billion
Accession: SCV002520966.1
First in ClinVar: Jun 03, 2022 Last updated: Jun 03, 2022 |
Comment:
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.050%). Frameshift: predicted to result in a loss … (more)
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.050%). Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000003309). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Lymphopenia (present) , Decreased helper T cell proportion (present) , Vitiligo (present) , Recurrent Haemophilus influenzae infections (present) , Arthralgia (present) , Onychomycosis (present) , … (more)
Lymphopenia (present) , Decreased helper T cell proportion (present) , Vitiligo (present) , Recurrent Haemophilus influenzae infections (present) , Arthralgia (present) , Onychomycosis (present) , Chronic oral candidiasis (present) , Chronic mucocutaneous candidiasis (present) (less)
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Pathogenic
(Nov 29, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329056.8
First in ClinVar: Dec 06, 2016 Last updated: Mar 04, 2023 |
Comment:
Considered to be a founder variant in the Anglo-American population (Pearce et al., 1998; Heino et al., 2001); Frameshift variant predicted to result in protein … (more)
Considered to be a founder variant in the Anglo-American population (Pearce et al., 1998; Heino et al., 2001); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies indicate the variant may have a minor dominant negative effect, which in heterozygotes could lead to atypical phenotypes with later onset and reduced penetrance (Oftedal et al., 2015); This variant is associated with the following publications: (PMID: 24948345, 19265170, 10677297, 27588307, 28769929, 28911151, 27219120, 11916620, 11207636, 19807739, 23620608, 9921903, 10720083, 17118990, 14557425, 26912174, 25707324, 9398840, 27253668, 28323927, 11298085, 31589614, 9837820, 26084028, 11524731) (less)
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Pathogenic
(Sep 14, 2023)
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criteria provided, single submitter
Method: clinical testing
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APECED
Affected status: yes
Allele origin:
germline
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National Institute of Allergy and Infectious Diseases - Centralized Sequencing Program, National Institutes of Health
Accession: SCV004036173.1
First in ClinVar: Sep 30, 2023 Last updated: Sep 30, 2023 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Polyglandular autoimmune syndrome, type 1
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004048245.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
Comment:
This sequence change creates a premature translational stop signal (p.Leu323Serfs*51) in the AIRE gene. This variant causes a frameshift starting with codon Leucine 323, changes … (more)
This sequence change creates a premature translational stop signal (p.Leu323Serfs*51) in the AIRE gene. This variant causes a frameshift starting with codon Leucine 323, changes this amino acid to Serine residue, and creates a premature Stop codon at position 51 of the new reading frame, denoted p.Leu323SerfsTer51. It is expected to result in an absent or disrupted protein product. This variant has been reported in numerous individuals and families affected with autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) and is the most common variant found in affected individuals of British or Anglo-American ancestry (Heino, Maarit, et al, Pearce, Simon HS, et al). An experimental study has shown that this sequence change has a dominant negative effect on the gene regulation of tested AIRE-regulated genes (Oftedal, Bergithe E., et al). This variant has been reported to the ClinVar database as Pathogenic/ Likely pathogenic. The variant is reported with the allele frequency of 0.05032% in gnomAD Exome is novel (not in any individuals) in 1000 Genomes. For these reasons, this variant has been classified as pathogenic (less)
Clinical Features:
Renal tubular acidosis (present) , Polyuria (present) , Polydipsia (present) , Metabolic acidosis (present) , Hypokalemia (present)
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probable-pathogenic
(-)
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no assertion criteria provided
Method: not provided
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Polyglandular autoimmune syndrome, type 1
Affected status: not provided
Allele origin:
unknown
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Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082042.1
First in ClinVar: Jul 24, 2013 Last updated: Jul 24, 2013
Comment:
FinDis database variant: FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference
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Comment:
Converted during submission to Likely pathogenic.
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Polyglandular autoimmune syndrome type 1
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001457181.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742992.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001932897.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(Nov 01, 2009)
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no assertion criteria provided
Method: literature only
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AUTOIMMUNE POLYENDOCRINOPATHY SYNDROME, TYPE I
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000023630.4
First in ClinVar: Apr 04, 2013 Last updated: Jun 17, 2024 |
Comment on evidence:
In studies of 16 North American cases of autoimmune polyendocrinopathy syndrome type I (APS1; 240300), Heino et al. (1999) found that a 1094-1106del mutation accounted … (more)
In studies of 16 North American cases of autoimmune polyendocrinopathy syndrome type I (APS1; 240300), Heino et al. (1999) found that a 1094-1106del mutation accounted for 17 of 32 alleles. The deletion of 13 nucleotides accounted for 5 of 18 northern Italian alleles (Finnish-German APECED Consortium, 1997). This mutation is the same as that designated 964del13 by Pearce et al. (1998) and 967-979del13 by Heino et al. (2001). In 9 of 16 patients with APS1, Wang et al. (1998) found a 13-bp deletion (1094-1106del) in exon 8 of the AIRE gene; 7 were homozygotes and 2 compound heterozygotes. Nithiyananthan et al. (2000) stated that the 13-bp deletion at nucleotide 964 in exon 8 (964del13) of the AIRE gene on chromosome 21q22.3 accounts for more than 70% of mutant alleles in United Kingdom subjects with APECED. The authors concluded that this mutation is not a susceptibility locus for the more common autoimmune endocrinopathies in the United Kingdom. In a patient diagnosed by Brodehl et al. (1967) with isolated hypercystinuria (see 220100) who was subsequently found to have autoimmune polyendocrinopathy type I, Eggermann et al. (2007) identified compound heterozygosity for the common mutations R257X (607358.0001) and 964del13. Two older sibs had died from hypocalcemic tetany. Wolff et al. (2007) found that this mutation was the most prevalent in Norwegian patients with APS1; it was present in 23 of 48 alleles. Harris et al. (2003) described 2 unrelated children with, in addition to APECED, a progressive skeletal deformity that spontaneously resolved in the mid-teen years. Both children carried the 964del13 mutation, one in homozygosity and the other in compound heterozygosity with a 1-bp deletion (607358.0009). In 4 patients with APS1 from 3 Indian families from unrelated caste groups, Zaidi et al. (2009) identified homozygosity for the 13-bp deletion, which they called 967_979del13. The parents were all heterozygous for the mutation. One patient, a 4-year-old girl who presented at age 2 years with type 1 diabetes mellitus (222100), died of septicemia. In 3 sibs with hypoparathyroidism, including a sister who had premature ovarian failure, Li et al. (2017) identified compound heterozygous mutation in the AIRE gene: the recurrent 13-bp deletion (607358.0003) and a splicing mutation (c.995+(3_5)delGAGinsTAT; 607358.0012). Their unaffected parents were each heterozygous for 1 of the mutations, and unaffected offspring were either heterozygous or wildtype. Noting that the patients were in the sixth and seventh decades of life, and that multiple manifestations of APS1 would normally have developed by the fifth decade of life, the authors stated that it was unclear why 2 of the 3 patients had such a limited APS1 phenotype. However, the near-constant development of hypoparathyroidism in APS1 suggested that parathyroid involvement occurs at a very low threshold and represents a very mild expression of the disease. In 2 unrelated children, aged 11 and 16 years, who exhibited apparent isolated hypoparathyroidism, Cranston et al. (2022) identified homozygosity for the 13-bp deletion in the AIRE gene. The authors noted that autoimmune parathyroid gland destruction represents an early manifestation of APS1, with a peak incidence at around 5 years of age, and suggested that the probands might well develop additional features of APS1. (less)
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Pathogenic
(Nov 01, 2009)
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no assertion criteria provided
Method: literature only
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AUTOIMMUNE POLYENDOCRINOPATHY SYNDROME, TYPE I, WITH REVERSIBLE METAPHYSEAL DYSPLASIA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000023631.4
First in ClinVar: Apr 04, 2013 Last updated: Jun 17, 2024 |
Comment on evidence:
In studies of 16 North American cases of autoimmune polyendocrinopathy syndrome type I (APS1; 240300), Heino et al. (1999) found that a 1094-1106del mutation accounted … (more)
In studies of 16 North American cases of autoimmune polyendocrinopathy syndrome type I (APS1; 240300), Heino et al. (1999) found that a 1094-1106del mutation accounted for 17 of 32 alleles. The deletion of 13 nucleotides accounted for 5 of 18 northern Italian alleles (Finnish-German APECED Consortium, 1997). This mutation is the same as that designated 964del13 by Pearce et al. (1998) and 967-979del13 by Heino et al. (2001). In 9 of 16 patients with APS1, Wang et al. (1998) found a 13-bp deletion (1094-1106del) in exon 8 of the AIRE gene; 7 were homozygotes and 2 compound heterozygotes. Nithiyananthan et al. (2000) stated that the 13-bp deletion at nucleotide 964 in exon 8 (964del13) of the AIRE gene on chromosome 21q22.3 accounts for more than 70% of mutant alleles in United Kingdom subjects with APECED. The authors concluded that this mutation is not a susceptibility locus for the more common autoimmune endocrinopathies in the United Kingdom. In a patient diagnosed by Brodehl et al. (1967) with isolated hypercystinuria (see 220100) who was subsequently found to have autoimmune polyendocrinopathy type I, Eggermann et al. (2007) identified compound heterozygosity for the common mutations R257X (607358.0001) and 964del13. Two older sibs had died from hypocalcemic tetany. Wolff et al. (2007) found that this mutation was the most prevalent in Norwegian patients with APS1; it was present in 23 of 48 alleles. Harris et al. (2003) described 2 unrelated children with, in addition to APECED, a progressive skeletal deformity that spontaneously resolved in the mid-teen years. Both children carried the 964del13 mutation, one in homozygosity and the other in compound heterozygosity with a 1-bp deletion (607358.0009). In 4 patients with APS1 from 3 Indian families from unrelated caste groups, Zaidi et al. (2009) identified homozygosity for the 13-bp deletion, which they called 967_979del13. The parents were all heterozygous for the mutation. One patient, a 4-year-old girl who presented at age 2 years with type 1 diabetes mellitus (222100), died of septicemia. In 3 sibs with hypoparathyroidism, including a sister who had premature ovarian failure, Li et al. (2017) identified compound heterozygous mutation in the AIRE gene: the recurrent 13-bp deletion (607358.0003) and a splicing mutation (c.995+(3_5)delGAGinsTAT; 607358.0012). Their unaffected parents were each heterozygous for 1 of the mutations, and unaffected offspring were either heterozygous or wildtype. Noting that the patients were in the sixth and seventh decades of life, and that multiple manifestations of APS1 would normally have developed by the fifth decade of life, the authors stated that it was unclear why 2 of the 3 patients had such a limited APS1 phenotype. However, the near-constant development of hypoparathyroidism in APS1 suggested that parathyroid involvement occurs at a very low threshold and represents a very mild expression of the disease. In 2 unrelated children, aged 11 and 16 years, who exhibited apparent isolated hypoparathyroidism, Cranston et al. (2022) identified homozygosity for the 13-bp deletion in the AIRE gene. The authors noted that autoimmune parathyroid gland destruction represents an early manifestation of APS1, with a peak incidence at around 5 years of age, and suggested that the probands might well develop additional features of APS1. (less)
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Pathogenic
(Jul 17, 2024)
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no assertion criteria provided
Method: clinical testing
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AIRE-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004115444.2
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
The AIRE c.967_979del13 variant is predicted to result in a frameshift and premature protein termination (p.Leu323Serfs*51). This variant has been reported in many unrelated individuals … (more)
The AIRE c.967_979del13 variant is predicted to result in a frameshift and premature protein termination (p.Leu323Serfs*51). This variant has been reported in many unrelated individuals to be pathogenic for autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) (Finnish-German APECED Consortium. 1997. PubMed ID: 9398840). This variant is reported in 0.096% of alleles in individuals of European (non-Finnish) descent in gnomAD and is interpreted as pathogenic or likely pathogenic by many labs in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/3309). Frameshift variants in AIRE are expected to be pathogenic. This variant is interpreted as pathogenic for autosomal recessive APECED. (less)
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not provided
(-)
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no classification provided
Method: phenotyping only
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Polyglandular autoimmune syndrome, type 1
Affected status: unknown
Allele origin:
paternal
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GenomeConnect - Invitae Patient Insights Network
Accession: SCV001749902.1
First in ClinVar: Jul 18, 2021 Last updated: Jul 18, 2021 |
Comment:
Variant interpreted as Pathogenic and reported on 11-09-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report … (more)
Variant interpreted as Pathogenic and reported on 11-09-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. (less)
Clinical Features:
Lymphadenopathy (present) , Abnormality of the immune system (present) , Mastocytosis (present) , Recurrent infections (present) , Epistaxis (present) , Gastroesophageal reflux (present) , Rhinitis … (more)
Lymphadenopathy (present) , Abnormality of the immune system (present) , Mastocytosis (present) , Recurrent infections (present) , Epistaxis (present) , Gastroesophageal reflux (present) , Rhinitis (present) , Tachycardia (present) , Dry skin (present) , Chest tightness (present) , Fatigue (present) , Cardiac arrhythmia (present) , Edema (present) , Inflammatory abnormality of the skin (present) , Allergic rhinitis (present) , Xerostomia (present) , Arthralgia (present) , Immunodeficiency (present) , Cough (present) , Dyspnea (present) , Orthostatic tachycardia (present) , Headache (present) , Fever (present) , Asthma (present) , Sepsis (present) , Nausea (present) , Allergy (present) , Vomiting (present) , Skin ulcer (present) , Facial erythema (present) , Urticaria (present) , Chronic oral candidiasis (present) , Vocal cord dysfunction (present) , Pruritus (present) , Skin rash (present) (less)
Indication for testing: Diagnostic
Age: 20-29 years
Sex: female
Testing laboratory: Invitae
Date variant was reported to submitter: 2020-11-09
Testing laboratory interpretation: Pathogenic
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Clinical exome sequencing of 1000 families with complex immune phenotypes: Toward comprehensive genomic evaluations. | Similuk MN | The Journal of allergy and clinical immunology | 2022 | PMID: 35753512 |
Spectrum of germline AIRE mutations causing APS-1 and familial hypoparathyroidism. | Cranston T | European journal of endocrinology | 2022 | PMID: 35521792 |
Expanding the Phenotypic and Genotypic Landscape of Autoimmune Polyendocrine Syndrome Type 1. | Orlova EM | The Journal of clinical endocrinology and metabolism | 2017 | PMID: 28911151 |
Exome Sequencing Reveals Mutations in AIRE as a Cause of Isolated Hypoparathyroidism. | Li D | The Journal of clinical endocrinology and metabolism | 2017 | PMID: 28323927 |
Redefined clinical features and diagnostic criteria in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. | Ferre EM | JCI insight | 2016 | PMID: 27588307 |
Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. | Kisand K | Journal of clinical immunology | 2015 | PMID: 26141571 |
Dominant Mutations in the Autoimmune Regulator AIRE Are Associated with Common Organ-Specific Autoimmune Diseases. | Oftedal BE | Immunity | 2015 | PMID: 26084028 |
Expanding the spectrum: chronic urticaria and autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. | Lundberg C | Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology | 2015 | PMID: 25707324 |
Clinical phenotypes of autoimmune polyendocrinopathycandidiasis-ectodermal dystrophy seen in the Northern Ireland paediatric population over the last 30 years. | Millar S | The Ulster medical journal | 2012 | PMID: 23620608 |
Clinical heterogeneity and diagnostic delay of autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy syndrome. | Mazza C | Clinical immunology (Orlando, Fla.) | 2011 | PMID: 21295522 |
Autoimmune polyglandular syndrome type 1 in Russian patients: clinical variants and autoimmune regulator mutations. | Orlova EM | Hormone research in paediatrics | 2010 | PMID: 20407228 |
Two novel AIRE mutations in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) among Indians. | Zaidi G | Clinical genetics | 2009 | PMID: 19807739 |
Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype. | Hubert FX | Journal of immunology (Baltimore, Md. : 1950) | 2009 | PMID: 19265170 |
Evaluation of the autoimmune regulator (AIRE) gene mutations in a cohort of Italian patients with autoimmune-polyendocrinopathy-candidiasis-ectodermal-dystrophy (APECED) and in their relatives. | Cervato S | Clinical endocrinology | 2009 | PMID: 18616706 |
Autoimmune polyendocrine syndrome type I in Slovakia: relevance of screening patients with autoimmune Addison's disease. | F Magitta N | European journal of endocrinology | 2008 | PMID: 18426830 |
Isolated cystinuria (OMIM 238200) is not a separate entity but is caused by a mutation in the cystinuria gene SLC7A9. | Eggermann T | Clinical genetics | 2007 | PMID: 17539912 |
Autoimmune polyendocrine syndrome type 1 in Norway: phenotypic variation, autoantibodies, and novel mutations in the autoimmune regulator gene. | Wolff AS | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17118990 |
Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) in the Irish population. | Dominguez M | Journal of pediatric endocrinology & metabolism : JPEM | 2006 | PMID: 17220063 |
Molecular background of polyendocrinopathy-candidiasis-ectodermal dystrophy syndrome in a Polish population: novel AIRE mutations and an estimate of disease prevalence. | Stolarski B | Clinical genetics | 2006 | PMID: 16965330 |
Reversible metaphyseal dysplasia, a novel bone phenotype, in two unrelated children with autoimmunepolyendocrinopathy-candidiasis-ectodermal dystrophy: clinical and molecular studies. | Harris M | The Journal of clinical endocrinology and metabolism | 2003 | PMID: 14557425 |
AIRE mutations and human leukocyte antigen genotypes as determinants of the autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy phenotype. | Halonen M | The Journal of clinical endocrinology and metabolism | 2002 | PMID: 12050215 |
Novel AIRE mutations and P450 cytochrome autoantibodies in Central and Eastern European patients with APECED. | Cihakova D | Human mutation | 2001 | PMID: 11524733 |
APECED mutations in the autoimmune regulator (AIRE) gene. | Heino M | Human mutation | 2001 | PMID: 11524731 |
Screening for an AIRE-1 mutation in patients with Addison's disease, type 1 diabetes, Graves' disease and Hashimoto's thyroiditis as well as in APECED syndrome. | Meyer G | Clinical endocrinology | 2001 | PMID: 11298085 |
Autoimmune polyendocrine syndrome type 1 (APS I) in Norway. | Myhre AG | Clinical endocrinology | 2001 | PMID: 11207636 |
A heterozygous deletion of the autoimmune regulator (AIRE1) gene, autoimmune thyroid disease, and type 1 diabetes: no evidence for association. | Nithiyananthan R | The Journal of clinical endocrinology and metabolism | 2000 | PMID: 10720083 |
Mutations in the AIRE gene: effects on subcellular location and transactivation function of the autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy protein. | Björses P | American journal of human genetics | 2000 | PMID: 10677297 |
Mutation analyses of North American APS-1 patients. | Heino M | Human mutation | 1999 | PMID: 9888391 |
Characterization of mutations in patients with autoimmune polyglandular syndrome type 1 (APS1). | Wang CY | Human genetics | 1998 | PMID: 9921903 |
A common and recurrent 13-bp deletion in the autoimmune regulator gene in British kindreds with autoimmune polyendocrinopathy type 1. | Pearce SH | American journal of human genetics | 1998 | PMID: 9837820 |
An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHD-type zinc-finger domains. | Finnish-German APECED Consortium | Nature genetics | 1997 | PMID: 9398840 |
[An isolated defect of the tubular cystine reabsorption in a family with idiopathic hypoparathyroidism]. | Brodehl J | Klinische Wochenschrift | 1967 | PMID: 6031738 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=AIRE | - | - | - | - |
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Text-mined citations for rs386833675 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.