NM_003673.4(TCAP):c.49C>T (p.Arg17Cys) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001045930.5

Allele description [Variation Report for NM_003673.4(TCAP):c.49C>T (p.Arg17Cys)]

NM_003673.4(TCAP):c.49C>T (p.Arg17Cys)

Gene:

TCAP:titin-cap [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_003673.4(TCAP):c.49C>T (p.Arg17Cys)

HGVS:

NC_000017.11:g.39665408C>T
NG_008892.1:g.5063C>T
NG_042278.1:g.2428C>T
NM_003673.4:c.49C>TMANE SELECT
NP_003664.1:p.Arg17Cys
NP_003664.1:p.Arg17Cys
LRG_210t1:c.49C>T
LRG_210:g.5063C>T
LRG_210p1:p.Arg17Cys
NC_000017.10:g.37821661C>T
NM_003673.3:c.49C>T

Protein change:

R17C

Links:

dbSNP: rs869025530

NCBI 1000 Genomes Browser:

rs869025530

Molecular consequence:

NM_003673.4:c.49C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hypertrophic cardiomyopathy 25 (CMH25)
Synonyms:: CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 25
Identifiers:: MONDO: MONDO:0011843; MedGen: C4225408; OMIM: 607487

Name:: Primary familial hypertrophic cardiomyopathy (HCM)
Synonyms:: Hereditary ventricular hypertrophy; Idiopathic hypertrophic subaortic stenosis
Identifiers:: MONDO: MONDO:0024573; MeSH: D024741; MedGen: C0949658; OMIM: PS192600

Recent activity

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AGENCOURT_8670864 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:4681490 5', mRN...
AGENCOURT_8670864 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:4681490 5', mRNA sequence
gi|22278009|gnl|dbEST|13177994|gb|B 95.1|

Nucleotide
JGI_CAAJ22961.rev NIH_XGC_tropBrn2 Xenopus tropicalis cDNA clone IMAGE:7650344 3...
JGI_CAAJ22961.rev NIH_XGC_tropBrn2 Xenopus tropicalis cDNA clone IMAGE:7650344 3', mRNA sequence
gi|71463739|gnl|dbEST|30357047|gb|C 52.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001209805	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 3, 2022)	germline	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

SCV001209805

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 3, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001209805.4

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

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 17 of the TCAP protein (p.Arg17Cys). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with TCAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 222830). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C35"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

Last Updated: Oct 8, 2024

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