VCV002159413.3 - ClinVar

NM_001142416.2(AIMP1):c.191_192del (p.Gln64fs)

Germline

Classification

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.

(2)

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.

Pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001142416.2(AIMP1):c.191_192del (p.Gln64fs)

Variation ID: 2159413 Accession: VCV002159413.3

Type and length

Deletion, 2 bp

Location

Cytogenetic: 4q24 4: 106327532-106327533 (GRCh38) [ NCBI UCSC ] 4: 107248689-107248690 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Feb 8, 2023	Feb 20, 2024	Nov 2, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001142416.2:c.191_192del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001135888.2:p.Gln64fs	frameshift
NM_001142415.2:c.191_192del	NP_001135887.1:p.Gln64fs	frameshift
NM_004757.4:c.191_192del	NP_004748.2:p.Gln64fs	frameshift
NM_004757.4:c.191_192delAA
NC_000004.12:g.106327532_106327533del
NC_000004.11:g.107248689_107248690del
NG_028166.1:g.16923_16924del

... more HGVS ... less HGVS

Protein change

Q64fs

Other names

Canonical SPDI

NC_000004.12:106327531:AA:

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

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
Gene	OMIM	HI score Help 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.
AIMP1		-	-	GRCh38 GRCh37	113	136

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.
not provided	Pathogenic (1)	criteria provided, single submitter	Aug 6, 2022	RCV003085941.3
Hypomyelinating leukodystrophy 3	Pathogenic (1)	criteria provided, single submitter	Nov 2, 2023	RCV003479471.1

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.
Pathogenic (Nov 02, 2023)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	Hypomyelinating leukodystrophy 3 Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV004222717.1 First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024	Publications: PubMed (2) PubMed: 30486714‚ 31618474 Comment: Variant summary: SCYE1 c.191_192delAA (p.Gln64ArgfsX25) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, a commonly … (more) Variant summary: SCYE1 c.191_192delAA (p.Gln64ArgfsX25) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, a commonly known mechanism for disease. The variant allele was found at a frequency of 2e-05 in 250996 control chromosomes (gnomAD). c.191_192delAA has been reported in the literature as a biallelic genotype in individuals with clinical phenotypes consistent with Hypomyelinating Leukodystrophy 3 (e.g. Accogli_2019, Burgess_2019). These data indicate that the variant is very likely associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 30486714, 31618474). One submitter has cited a clinical-significance assessment for this variant to ClinVar after 2014 and has classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
Pathogenic (Aug 06, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003472482.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Publications: PubMed (3) PubMed: 30486714‚ 31618474‚ 21092922 Comment: For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.263_264del. This premature translational stop signal has been observed … (more) For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.263_264del. This premature translational stop signal has been observed in individual(s) with AIMP1-related conditions (PMID: 30486714, 31618474). This variant is present in population databases (rs766457850, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Gln64Argfs*25) in the AIMP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AIMP1 are known to be pathogenic (PMID: 21092922). (less)

Comment:

Variant summary: SCYE1 c.191_192delAA (p.Gln64ArgfsX25) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, a commonly known mechanism for disease. The variant allele was found at a frequency of 2e-05 in 250996 control chromosomes (gnomAD). c.191_192delAA has been reported in the literature as a biallelic genotype in individuals with clinical phenotypes consistent with Hypomyelinating Leukodystrophy 3 (e.g. Accogli_2019, Burgess_2019). These data indicate that the variant is very likely associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 30486714, 31618474). One submitter has cited a clinical-significance assessment for this variant to ClinVar after 2014 and has classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Comment:

For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.263_264del. This premature translational stop signal has been observed in individual(s) with AIMP1-related conditions (PMID: 30486714, 31618474). This variant is present in population databases (rs766457850, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Gln64Argfs*25) in the AIMP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AIMP1 are known to be pathogenic (PMID: 21092922).

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
The Genetic Landscape of Epilepsy of Infancy with Migrating Focal Seizures.	Burgess R	Annals of neurology	2019	PMID: 31618474
Biallelic Loss-of-Function Variants in AIMP1 Cause a Rare Neurodegenerative Disease.	Accogli A	Journal of child neurology	2019	PMID: 30486714
Pelizaeus-Merzbacher-like disease caused by AIMP1/p43 homozygous mutation.	Feinstein M	American journal of human genetics	2010	PMID: 21092922

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001142416.2(AIMP1):c.191_192del (p.Gln64fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...