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NM_001256317.3(TMPRSS3):c.268G>A (p.Ala90Thr) AND Autosomal recessive nonsyndromic hearing loss 8

Germline classification:
Benign/Likely benign (3 submissions)
Last evaluated:
Nov 29, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000999777.14

Allele description [Variation Report for NM_001256317.3(TMPRSS3):c.268G>A (p.Ala90Thr)]

NM_001256317.3(TMPRSS3):c.268G>A (p.Ala90Thr)

Gene:
TMPRSS3:transmembrane serine protease 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_001256317.3(TMPRSS3):c.268G>A (p.Ala90Thr)
HGVS:
  • NC_000021.9:g.42388983C>T
  • NG_011629.2:g.12109G>A
  • NM_001256317.3:c.268G>AMANE SELECT
  • NM_024022.4:c.268G>A
  • NM_032404.3:c.-114G>A
  • NM_032405.2:c.268G>A
  • NP_001243246.1:p.Ala90Thr
  • NP_076927.1:p.Ala90Thr
  • NP_115781.1:p.Ala90Thr
  • NC_000021.8:g.43809092C>T
  • NM_024022.2:c.268G>A
  • NM_024022.3:c.268G>A
  • c.268G>A
Protein change:
A90T
Links:
dbSNP: rs45598239
NCBI 1000 Genomes Browser:
rs45598239
Molecular consequence:
  • NM_032404.3:c.-114G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001256317.3:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024022.4:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032405.2:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 8
Synonyms:
NEUROSENSORY NONSYNDROMIC RECESSIVE DEAFNESS 8; Deafness, autosomal recessive 8; Deafness, autosomal recessive 10
Identifiers:
MONDO: MONDO:0010987; MedGen: C1832827; Orphanet: 90636; OMIM: 601072

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000605388ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Benign
(Nov 29, 2023)
germlineclinical testing

Citation Link,

SCV001300981Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Likely benign
(Apr 27, 2017)
germlineclinical testing

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

Citation Link,

SCV002802971Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(May 20, 2022)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Assessment of the genetic causes of recessive childhood non-syndromic deafness in the UK - implications for genetic testing.

Hutchin T, Coy NN, Conlon H, Telford E, Bromelow K, Blaydon D, Taylor G, Coghill E, Brown S, Trembath R, Liu XZ, Bitner-Glindzicz M, Mueller R.

Clin Genet. 2005 Dec;68(6):506-12.

PubMed [citation]
PMID:
16283880

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000605388.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001300981.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

From Fulgent Genetics, Fulgent Genetics, SCV002802971.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 10, 2024