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NM_001001331.4(ATP2B2):c.1891G>A (p.Val631Met) AND Deafness, autosomal recessive 12, modifier of

Germline classification:
risk factor (1 submission)
Last evaluated:
Apr 14, 2005
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000019379.25

Allele description [Variation Report for NM_001001331.4(ATP2B2):c.1891G>A (p.Val631Met)]

NM_001001331.4(ATP2B2):c.1891G>A (p.Val631Met)

Gene:
ATP2B2:ATPase plasma membrane Ca2+ transporting 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_001001331.4(ATP2B2):c.1891G>A (p.Val631Met)
HGVS:
  • NC_000003.12:g.10359892C>T
  • NG_012046.2:g.353140G>A
  • NM_001001331.4:c.1891G>AMANE SELECT
  • NM_001330611.3:c.1756G>A
  • NM_001353564.1:c.1756G>A
  • NM_001363862.1:c.1756G>A
  • NM_001683.5:c.1756G>A
  • NP_001001331.1:p.Val631Met
  • NP_001317540.1:p.Val586Met
  • NP_001340493.1:p.Val586Met
  • NP_001350791.1:p.Val586Met
  • NP_001674.2:p.Val586Met
  • NC_000003.11:g.10401576C>T
  • NM_001683.3:c.1756G>A
Protein change:
V586M; VAL586MET
Links:
OMIM: 108733.0001; dbSNP: rs61736451
NCBI 1000 Genomes Browser:
rs61736451
Molecular consequence:
  • NM_001001331.4:c.1891G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330611.3:c.1756G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353564.1:c.1756G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363862.1:c.1756G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001683.5:c.1756G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Deafness, autosomal recessive 12, modifier of
Identifiers:
MedGen: C4015888

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000039669OMIM
no assertion criteria provided
risk factor
(Apr 14, 2005) 		germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Modification of human hearing loss by plasma-membrane calcium pump PMCA2.

Schultz JM, Yang Y, Caride AJ, Filoteo AG, Penheiter AR, Lagziel A, Morell RJ, Mohiddin SA, Fananapazir L, Madeo AC, Penniston JT, Griffith AJ.

N Engl J Med. 2005 Apr 14;352(15):1557-64. Erratum in: N Engl J Med. 2005 Jun 2;352(22):2362.

PubMed [citation]
PMID:
15829536

Analysis of protein-coding genetic variation in 60,706 humans.

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, et al.

Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057.

PubMed [citation]
PMID:
27535533
PMCID:
PMC5018207

Details of each submission

From OMIM, SCV000039669.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 3 of 5 sibs, born of consanguineous parents, with autosomal recessive deafness (DFNB12; 601386) caused by a homozygous phe1888-to-ser substitution in the CDH23 gene (F1888S; 605516.0010), Schultz et al. (2005) identified a heterozygous 2075G-A transition in exon 12 of the ATP2B2 gene, resulting in a val586-to-met (V586M) substitution. The 3 sibs heterozygous for V586M had severe to profound hearing loss affecting all frequencies, whereas the other 2 sibs had high-frequency hearing loss. Schultz et al. (2005) suggested that V586M modifies the severity of sensorineural hearing loss.

Lek et al. (2016) questioned the validity of this variant as a modifier of the severity of deafness because it has a high allele frequency (0.0467) in the Latino population in the ExAC database.

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

Last Updated: Apr 15, 2024