VCV002674617.1 - ClinVar

NM_013296.5(GPSM2):c.681+1G>A

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.

(1)

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.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_013296.5(GPSM2):c.681+1G>A

Variation ID: 2674617 Accession: VCV002674617.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1p13.3 1: 108898766 (GRCh38) [ NCBI UCSC ] 1: 109441388 (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	Dec 25, 2023	Dec 24, 2023	Dec 13, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NM_013296.5:c.681+1G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001321038.2:c.681+1G>A		splice donor
NM_001321039.3:c.681+1G>A		splice donor
NC_000001.11:g.108898766G>A
NC_000001.10:g.109441388G>A
NG_028108.2:g.28417G>A
LRG_1373:g.28417G>A
LRG_1373t1:c.681+1G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000001.11:108898765:G:A

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.
GPSM2		-	-	GRCh38 GRCh37	230	307

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.
Chudley-McCullough syndrome	Likely pathogenic (1)	criteria provided, single submitter	Dec 13, 2021	RCV003456354.1

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.
Likely pathogenic (Dec 13, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Chudley-McCullough syndrome (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center Accession: SCV004190164.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023	Publications: PubMed (1) PubMed: 22578326 Comment: To the best of our knowledge, this variant has not been reported in the literature. However, it is a heterozygous canonical splice site variant, which … (more) To the best of our knowledge, this variant has not been reported in the literature. However, it is a heterozygous canonical splice site variant, which is expected to affect splicing and results in a null effect. Homozygous or compound heterozygous loss-of-function variants in GPSM2 have been reported in patient cohorts with Chudley-McCullough syndrome (PMID: 22578326). This variant has been observed in the Genome Aggregation Database (gnomAD) at a very low frequency (1/251,398), indicating it is not a common benign variant in the populations represented in this database. (less) Age: 10-19 weeks gestation Ethnicity/Population group: Hispanic Americans Geographic origin: Mexico Tissue: CVS Comment on evidence: Observed in trans with c.1062+1G>T

Comment:

To the best of our knowledge, this variant has not been reported in the literature. However, it is a heterozygous canonical splice site variant, which is expected to affect splicing and results in a null effect. Homozygous or compound heterozygous loss-of-function variants in GPSM2 have been reported in patient cohorts with Chudley-McCullough syndrome (PMID: 22578326). This variant has been observed in the Genome Aggregation Database (gnomAD) at a very low frequency (1/251,398), indicating it is not a common benign variant in the populations represented in this database.

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
GPSM2 mutations cause the brain malformations and hearing loss in Chudley-McCullough syndrome.	Doherty D	American journal of human genetics	2012	PMID: 22578326

Text-mined citations for this variant ...

Record last updated Dec 30, 2023

ClinVar Genomic variation as it relates to human health

NM_013296.5(GPSM2):c.681+1G>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...