Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_013296.5(GPSM2):c.1473del (p.Phe492fs)

Help
Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Mar 21, 2019)
Last evaluated:
Apr 27, 2017
Accession:
VCV000291707.2
Variation ID:
291707
Description:
1bp deletion
Help

NM_013296.5(GPSM2):c.1473del (p.Phe492fs)

Allele ID
275828
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
1p13.3
Genomic location
1: 108922447 (GRCh38) GRCh38 UCSC
1: 109465069 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.109465071del
NC_000001.11:g.108922449del
NM_013296.5:c.1473del MANE Select NP_037428.3:p.Phe492fs
... more HGVS
Protein change
F492fs
Other names
-
Canonical SPDI
NC_000001.11:108922446:GGG:GG
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA983068
dbSNP: rs772372530
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter May 6, 2016 RCV000224236.1
Pathogenic 1 criteria provided, single submitter Apr 27, 2017 RCV000380707.2
Pathogenic 1 criteria provided, single submitter Jun 9, 2016 RCV000607932.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GPSM2 - - GRCh38
GRCh37
140 187

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 06, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281030.1
Submitted: (May 19, 2016)
Evidence details
Pathogenic
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
GPSM2-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000347062.3
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (3)
Comment:
The GPSM2 c.1473delG (p.Phe492SerfsTer5) variant, also referred to as c.1471delG, results in a frameshift and is predicted to cause a premature truncation of the protein. … (more)
Pathogenic
(Jun 09, 2016)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000712254.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (4)
Comment:
The p.Phe492fs variant in GPSM2 has been previously reported in 6 homozygous ind ividuals with Chudley McCullough syndrome (CMS) and 1 homozygous individual with sensorineural … (more)

Functional evidence

Help
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 this variant

Help
Title Author Journal Year Link
GPSM2 and Chudley-McCullough syndrome: a Dutch founder variant brought to North America. Almomani R American journal of medical genetics. Part A 2013 PMID: 23494849
A sensitive and specific diagnostic test for hearing loss using a microdroplet PCR-based approach and next generation sequencing. Schrauwen I American journal of medical genetics. Part A 2013 PMID: 23208854
GPSM2 mutations cause the brain malformations and hearing loss in Chudley-McCullough syndrome. Doherty D American journal of human genetics 2012 PMID: 22578326
Bilateral sensorineural deafness, partial agenesis of the corpus callosum, and arachnoid cysts in two sisters. Hendriks YM American journal of medical genetics 1999 PMID: 10449658

Text-mined citations for rs772372530...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jul 07, 2021