ClinVar Genomic variation as it relates to human health
NM_001042492.3(NF1):c.7549C>T (p.Arg2517Ter)
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_001042492.3(NF1):c.7549C>T (p.Arg2517Ter)
Variation ID: 230467 Accession: VCV000230467.88
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 17q11.2 17: 31352348 (GRCh38) [ NCBI UCSC ] 17: 29679366 (GRCh37) [ 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 May 29, 2016 May 12, 2024 Dec 13, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001042492.3:c.7549C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001035957.1:p.Arg2517Ter nonsense NM_000267.3:c.7486C>T NP_000258.1:p.Arg2496Ter nonsense NC_000017.11:g.31352348C>T NC_000017.10:g.29679366C>T NG_009018.1:g.262372C>T LRG_214:g.262372C>T LRG_214t1:c.7486C>T LRG_214p1:p.Arg2496Ter LRG_214t2:c.7549C>T LRG_214p2:p.Arg2517Ter - Protein change
- R2496*, R2517*
- Other names
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- Canonical SPDI
- NC_000017.11:31352347:C:T
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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
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The frequency of the allele represented by this VCV record.
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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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NF1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
13560 | 13967 |
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) |
criteria provided, single submitter
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Feb 18, 2015 | RCV000218957.2 | |
Pathogenic (11) |
criteria provided, multiple submitters, no conflicts
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Dec 13, 2023 | RCV000457951.25 | |
Pathogenic (1) |
criteria provided, single submitter
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Nov 16, 2016 | RCV000505900.9 | |
Pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Jan 16, 2023 | RCV000579098.26 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 10, 2021 | RCV001836756.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 24, 2022 | RCV003469003.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 11, 2022 | RCV002494586.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 30, 2023 | RCV003595895.1 |
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
(Nov 16, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000604508.1
First in ClinVar: Sep 30, 2017 Last updated: Sep 30, 2017 |
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Pathogenic
(Nov 01, 2016)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
germline
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Center for Human Genetics, Inc, Center for Human Genetics, Inc
Accession: SCV000782105.1
First in ClinVar: Jul 07, 2018 Last updated: Jul 07, 2018 |
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Pathogenic
(May 25, 2018)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000917894.1
First in ClinVar: May 31, 2019 Last updated: May 31, 2019 |
Comment:
Variant summary: NF1 c.7486C>T (p.Arg2496X) results in a premature termination codon, predicted to cause a truncation of the encoded protein (12%) or absence of the … (more)
Variant summary: NF1 c.7486C>T (p.Arg2496X) results in a premature termination codon, predicted to cause a truncation of the encoded protein (12%) or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 121268 control chromosomes. The c.7486C>T has been reported in the literature in multiple individuals affected with Neurofibromatosis Type 1, both in sporadic and familial cases. These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four 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
(Feb 18, 2015)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000274026.4
First in ClinVar: May 29, 2016 Last updated: May 29, 2016 |
Comment:
The p.R2517* pathogenic mutation (also known as c.7549C>T) located in coding exon 51 of the NF1 gene, results from a C to T substitution at … (more)
The p.R2517* pathogenic mutation (also known as c.7549C>T) located in coding exon 51 of the NF1 gene, results from a C to T substitution at nucleotide position 7549. This changes the amino acid from an arginine to a stop codon within coding exon 51. This mutation (reported as R2496X) has been detected in an individual with sporadic NF1 (Purandare S et al, Hum. Mol. Genet. 1994 Jul; 3(7):1109-15). In addition to the clinical data presented in the literature, since premature stop codons are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). (less)
Number of individuals with the variant: 1
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Pathogenic
(Oct 26, 2020)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV001479109.1
First in ClinVar: Feb 13, 2021 Last updated: Feb 13, 2021 |
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Pathogenic
(Jan 26, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV001879403.1
First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021 |
Comment:
This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with … (more)
This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. In some published literature, this variant is referred to as c.7549C>T; p.R2517X. (less)
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Pathogenic
(Jul 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Abnormality of the skin
Affected status: yes
Allele origin:
germline
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Kariminejad - Najmabadi Pathology & Genetics Center
Accession: SCV000927087.2
First in ClinVar: Jul 24, 2019 Last updated: Feb 20, 2022 |
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Pathogenic
(Mar 15, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV002560579.1
First in ClinVar: Aug 23, 2022 Last updated: Aug 23, 2022 |
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Pathogenic
(May 11, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
unknown
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Institute of Medical Genetics, University of Zurich
Accession: SCV002569046.2
First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023 |
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Pathogenic
(Sep 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
germline
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3billion
Accession: SCV002573296.1
First in ClinVar: Sep 17, 2022 Last updated: Sep 17, 2022 |
Comment:
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Stop-gained (nonsense) is predicted to result in … (more)
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Stop-gained (nonsense) is 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: VCV000230467 / PMID: 7981679). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Hydrocephalus (present) , Strabismus (present) , Cafe-au-lait spot (present) , Optic nerve glioma (present)
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Pathogenic
(Mar 14, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002580805.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022
Comment:
ACMG criteria applied: PVS1, PS4_MOD, PM2_SUP, PP4
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Number of individuals with the variant: 1
Sex: female
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Pathogenic
(Nov 18, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV002604943.2
First in ClinVar: Nov 19, 2022 Last updated: May 27, 2023 |
Clinical Features:
Neurofibromatosis (present) , Hypotonia (present) , Pes planus (present) , Delayed gross motor development (present) , Cafe au lait spots, multiple (present) , Inguinal freckling … (more)
Neurofibromatosis (present) , Hypotonia (present) , Pes planus (present) , Delayed gross motor development (present) , Cafe au lait spots, multiple (present) , Inguinal freckling (present) (less)
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Pathogenic
(Jan 26, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV002774393.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
Comment:
This nonsense variant causes the premature termination of NF1 protein synthesis. In addition, it has been reported in individuals affected with Neurofibromatosis type 1 in … (more)
This nonsense variant causes the premature termination of NF1 protein synthesis. In addition, it has been reported in individuals affected with Neurofibromatosis type 1 in the published literature (PMIDs: 29415745 (2018), 25324867 (2014), 22965773 (2012), 16835897 (2006), 10712197 (2000), 9783703 (1998), and 7981679 (1994)). Based on the available information, this variant is classified is pathogenic. (less)
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Pathogenic
(Mar 11, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Neurofibromatosis, familial spinal Café-au-lait macules with pulmonary stenosis Neurofibromatosis-Noonan syndrome Juvenile myelomonocytic leukemia
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002779142.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Aug 03, 2020)
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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: SCV000680726.5
First in ClinVar: Feb 13, 2018 Last updated: Mar 04, 2023 |
Comment:
Nonsense variant predicted to result in protein truncation in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with … (more)
Nonsense variant predicted to result in protein truncation in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 7981679, 27838393, 30530636, 25525159, 25324867, 26056819, 9783703, 10862084, 27930734, 18041031, 10712197, 11857752, 28135719, 22965773, 16835897, 18546366, 15060124, 29415745, 23460398, 10678181, 31766501, 30098238, 31776437) (less)
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Pathogenic
(Jul 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
unknown
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KCCC/NGS Laboratory, Kuwait Cancer Control Center
Accession: SCV004015244.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg2496*) in the NF1 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg2496*) in the NF1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD). This variant has been reported in individuals with neurofibromatosis type 1 (PMID: 25324867, 7981679, 22965773, 10712197, 16835897). This variant is also known as p.Arg2517* in the literature. ClinVar contains an entry for this variant (Variation ID: 230467) with 14 submissions. Loss-of-function variants in NF1 are known to be pathogenic (PMID: 10712197, 23913538). Therefore, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Oct 24, 2022)
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criteria provided, single submitter
Method: clinical testing
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Juvenile myelomonocytic leukemia
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004190784.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Jan 16, 2023)
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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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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV004224761.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
PP4, PM2, PVS1
Number of individuals with the variant: 19
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Pathogenic
(Oct 30, 2023)
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criteria provided, single submitter
Method: clinical testing
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NF1-related disorder
Affected status: yes
Allele origin:
germline
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Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV004244665.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
PVS1, PS4, PM2, PM6
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Pathogenic
(Dec 13, 2023)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000541947.10
First in ClinVar: Apr 17, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg2496*) in the NF1 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg2496*) in the NF1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NF1 are known to be pathogenic (PMID: 10712197, 23913538). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with neurofibromatosis type 1 (PMID: 7981679, 10712197, 16835897, 22965773, 25324867). This variant is also known as p.Arg2517*. ClinVar contains an entry for this variant (Variation ID: 230467). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 01, 2020)
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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: SCV001334647.20
First in ClinVar: Jun 08, 2020 Last updated: May 12, 2024 |
Number of individuals with the variant: 1
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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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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001955895.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 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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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001975568.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
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not provided
(-)
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no classification provided
Method: phenotyping only
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
unknown
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GenomeConnect, ClinGen
Accession: SCV000986762.1
First in ClinVar: Aug 30, 2019 Last updated: Aug 30, 2019 |
Comment:
Variant interpretted as pathogenic and reported on 02/09/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from … (more)
Variant interpretted as pathogenic and reported on 02/09/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less)
Clinical Features:
Abnormality of the skull (present) , Myopia (present) , Generalized hypotonia (present) , Multiple cafe-au-lait spots (present)
Age: 0-9 years
Sex: male
Method: Sanger Sequencing
Testing laboratory: GeneDx
Date variant was reported to submitter: 2018-02-09
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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Pathogenic NF1 truncating mutation and copy number alterations in a dedifferentiated liposarcoma with multiple lung metastasis: a case report. | Kim YS | BMC medical genetics | 2020 | PMID: 33046013 |
Phenotype categorization of neurofibromatosis type I and correlation to NF1 mutation types. | Kang E | Journal of human genetics | 2020 | PMID: 31776437 |
Breast cancer risk in neurofibromatosis type 1 is a function of the type of NF1 gene mutation: a new genotype-phenotype correlation. | Frayling IM | Journal of medical genetics | 2019 | PMID: 30530636 |
Cutaneous neurofibromas in Neurofibromatosis type I: a quantitative natural history study. | Cannon A | Orphanet journal of rare diseases | 2018 | PMID: 29415745 |
Mutation spectrum of NF1 gene in Italian patients with neurofibromatosis type 1 using Ion Torrent PGM™ platform. | Calì F | European journal of medical genetics | 2017 | PMID: 27838393 |
Neurofibromatosis type 1: a single center's experience in Korea. | Kim MJ | Korean journal of pediatrics | 2014 | PMID: 25324867 |
NF1 molecular characterization and neurofibromatosis type I genotype-phenotype correlation: the French experience. | Sabbagh A | Human mutation | 2013 | PMID: 23913538 |
Neurofibromatosis-1 gene deletions and mutations in de novo adult acute myeloid leukemia. | Boudry-Labis E | American journal of hematology | 2013 | PMID: 23460398 |
A new nonsense mutation in the NF1 gene with neurofibromatosis-Noonan syndrome phenotype. | Yimenicioğlu S | Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery | 2012 | PMID: 22965773 |
Identification of forty-five novel and twenty-three known NF1 mutations in Chinese patients with neurofibromatosis type 1. | Lee MJ | Human mutation | 2006 | PMID: 16835897 |
Minor lesion mutational spectrum of the entire NF1 gene does not explain its high mutability but points to a functional domain upstream of the GAP-related domain. | Fahsold R | American journal of human genetics | 2000 | PMID: 10712197 |
Nf1 and Gmcsf interact in myeloid leukemogenesis. | Birnbaum RA | Molecular cell | 2000 | PMID: 10678181 |
Neurofibromatosis type 1 (NF1): a protein truncation assay yielding identification of mutations in 73% of patients. | Park VM | Journal of medical genetics | 1998 | PMID: 9783703 |
Characterisation of inherited and sporadic mutations in neurofibromatosis type-1. | Purandare SM | Human molecular genetics | 1994 | PMID: 7981679 |
- | - | - | - | PMID: 125305868 |
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Text-mined citations for rs866445127 ...
HelpRecord last updated May 12, 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.