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

Recent activity

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SRX10016435 (1)
SRA
N-acetylmannosaminyltransferase [Lactobacillus acidophilus La-14]
N-acetylmannosaminyltransferase [Lactobacillus acidophilus La-14]
gi|488446483|gnl|Dupont|La14_0545|g 93726.1|

Protein
beta-glucosidase Bgl3D [Butyrivibrio proteoclasticus B316]
beta-glucosidase Bgl3D [Butyrivibrio proteoclasticus B316]
gi|302395924|gnl|agres|bpr_I2096|gb 4829.1|

Protein
Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain protein [Bacteroides...
Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain protein [Bacteroides xylanisolvens]
gi|2032864020|gnl|IGS|INE92_01068|g 29077.1|

Protein
maturase K, partial (plastid) [Zostera japonica]
maturase K, partial (plastid) [Zostera japonica]
gi|1046225848|gb|ANV28286.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000605388	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Nov 29, 2023)	germline	clinical testing	Citation Link,
SCV001300981	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002802971	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 20, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000605388

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Nov 29, 2023)

germline

clinical testing

Citation Link,

SCV001300981

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV002802971

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(May 20, 2022)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV001300981.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002802971.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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