NM_006383.4(CIB2):c.556C>T (p.Arg186Trp) AND Childhood onset hearing loss

Clinical significance:Likely pathogenic (Last evaluated: Jul 8, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001328027.2

Allele description [Variation Report for NM_006383.4(CIB2):c.556C>T (p.Arg186Trp)]

NM_006383.4(CIB2):c.556C>T (p.Arg186Trp)

Gene:
CIB2:calcium and integrin binding family member 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q25.1
Genomic location:
Preferred name:
NM_006383.4(CIB2):c.556C>T (p.Arg186Trp)
HGVS:
  • NC_000015.10:g.78105319G>A
  • NG_033006.1:g.31217C>T
  • NM_001271888.2:c.427C>T
  • NM_001271889.2:c.409C>T
  • NM_001301224.2:c.571C>T
  • NM_006383.4:c.556C>TMANE SELECT
  • NP_001258817.1:p.Arg143Trp
  • NP_001258818.1:p.Arg137Trp
  • NP_001288153.1:p.Arg191Trp
  • NP_006374.1:p.Arg186Trp
  • NC_000015.9:g.78397661G>A
  • NR_125435.2:n.764C>T
Protein change:
R137W
Links:
dbSNP: rs370359511
NCBI 1000 Genomes Browser:
rs370359511
Molecular consequence:
  • NM_001271888.2:c.427C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271889.2:c.409C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301224.2:c.571C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006383.4:c.556C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_125435.2:n.764C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Childhood onset hearing loss
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001519360National Institute on Deafness and Communication Disorders,National Institutes of Healthcriteria provided, single submitter
Likely pathogenic
(Jul 8, 2021)
germlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
African,Yorubagermlineyes2not providednot provided2yesresearch

Citations

PubMed

Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss.

Oza AM, DiStefano MT, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Murry JB, Hasadsri L, Nara K, Kenna M, Booth KT, Azaiez H, Griffith A, Avraham KB, Kremer H, Rehm HL, Amr SS, Abou Tayoun AN; et al.

Hum Mutat. 2018 Nov;39(11):1593-1613. doi: 10.1002/humu.23630.

PubMed [citation]
PMID:
30311386
PMCID:
PMC6188673

Details of each submission

From National Institute on Deafness and Communication Disorders,National Institutes of Health, SCV001519360.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1African,Yoruba1not providedyesresearch PubMed (1)
2African,Yoruba1not providedyesresearch PubMed (1)

Description

PS3_supporting, PM1, PM2_supporting, PM3_supporting, PP1_moderate / Modifications from PMID: 30311386 for classification: The genetic causes of hearing loss have not yet been well characterized in the Yoruba population, and the information regarding variant MAF in this population is still limited, so we did not exclude any variant based on their "high" MAF. PP3 criteria was applied even if the REVEL score was below 0.7, if at least two of the pathogenicity prediction algorithms used predicted that the variant was damaging or likely damaging.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided
2germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Jul 31, 2021

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