NM_001256317.3(TMPRSS3):c.757A>G (p.Ile253Val) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: May 9, 2017
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:: RCV000039366.12

Allele description [Variation Report for NM_001256317.3(TMPRSS3):c.757A>G (p.Ile253Val)]

NM_001256317.3(TMPRSS3):c.757A>G (p.Ile253Val)

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.757A>G (p.Ile253Val)

HGVS:

NC_000021.9:g.42383058T>C
NG_011629.2:g.18034A>G
NM_001256317.3:c.757A>GMANE SELECT
NM_024022.4:c.757A>G
NM_032404.3:c.376A>G
NM_032405.2:c.757A>G
NP_001243246.1:p.Ile253Val
NP_076927.1:p.Ile253Val
NP_115780.1:p.Ile126Val
NP_115781.1:p.Ile253Val
NC_000021.8:g.43803167T>C
NM_024022.2:c.757A>G
P57727:p.Ile253Val
c.757A>G

Protein change:

I126V

Links:

UniProtKB: P57727#VAR_013101; dbSNP: rs2839500

NCBI 1000 Genomes Browser:

rs2839500

Molecular consequence:

NM_001256317.3:c.757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_024022.4:c.757A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032404.3:c.376A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032405.2:c.757A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

552

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000063050	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Feb 16, 2007)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12920079, 24033266
SCV000314239	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000717808	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 9, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000063050

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Feb 16, 2007)

germline

clinical testing

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

SCV000314239

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

clinical testing

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

SCV000717808

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(May 9, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	559	552	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

Pathogenic mutations but not polymorphisms in congenital and childhood onset autosomal recessive deafness disrupt the proteolytic activity of TMPRSS3.

Lee YJ, Park D, Kim SY, Park WJ.

J Med Genet. 2003 Aug;40(8):629-31. No abstract available.

PubMed [citation]

PMID:: 12920079
PMCID:: PMC1735556

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

See all PubMed Citations (3)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000063050.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	559	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		559	not provided	552	not provided

From PreventionGenetics, part of Exact Sciences, SCV000314239.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV000717808.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

Last Updated: Sep 29, 2024

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