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NM_013296.5(GPSM2):c.1063-1G>T AND Rare genetic deafness

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 17, 2015
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000218080.4

Allele description [Variation Report for NM_013296.5(GPSM2):c.1063-1G>T]

NM_013296.5(GPSM2):c.1063-1G>T

Gene:
GPSM2:G protein signaling modulator 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p13.3
Genomic location:
Preferred name:
NM_013296.5(GPSM2):c.1063-1G>T
HGVS:
  • NC_000001.11:g.108904124G>T
  • NG_028108.2:g.33775G>T
  • NM_001321038.2:c.1063-1G>T
  • NM_001321039.3:c.1063-1G>T
  • NM_013296.5:c.1063-1G>TMANE SELECT
  • LRG_1373t1:c.1063-1G>T
  • LRG_1373:g.33775G>T
  • NC_000001.10:g.109446746G>T
  • NM_013296.4:c.1063-1G>T
Links:
dbSNP: rs773068151
NCBI 1000 Genomes Browser:
rs773068151
Molecular consequence:
  • NM_001321038.2:c.1063-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321039.3:c.1063-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_013296.5:c.1063-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

Condition(s)

Name:
Rare genetic deafness
Identifiers:
MedGen: C5680250; Orphanet: 96210

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000271378Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Pathogenic
(Sep 17, 2015) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000271378.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.1063-1G>T variant in GPSM2 has not been previously reported in individuals with hearing loss or Chudley-McCullough syndrome, but has been identified in 1/ 65476 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exa c.broadinstitute.org; dbSNP rs773068151). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a rec essive carrier frequency. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing lead ing to an abnormal or absent protein. Loss-of-function variants in the GPSM2 gen e are associated with Chudley-McCullough syndrome, an autosomal recessive condit ion with congenital hearing loss and brain abnormalities with typically normal c ognition. In summary, this variant meets our criteria to be classified as pathog enic for hearing loss in an autosomal recessive manner based on the predicted im pact of the variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Oct 8, 2024