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NM_001276345.2(TNNT2):c.347_348delinsCT (p.Ile116Thr) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 28, 2023
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:
RCV000646067.13

Allele description [Variation Report for NM_001276345.2(TNNT2):c.347_348delinsCT (p.Ile116Thr)]

NM_001276345.2(TNNT2):c.347_348delinsCT (p.Ile116Thr)

Gene:
TNNT2:troponin T2, cardiac type [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
1q32.1
Genomic location:
Preferred name:
NM_001276345.2(TNNT2):c.347_348delinsCT (p.Ile116Thr)
HGVS:
  • NC_000001.11:g.201365254_201365255delinsAG
  • NG_007556.1:g.17423_17424delinsCT
  • NM_000364.4:c.347_348delinsCT
  • NM_001001430.3:c.317_318delinsCT
  • NM_001001431.3:c.317_318delinsCT
  • NM_001001432.3:c.302_303delinsCT
  • NM_001276345.2:c.347_348delinsCTMANE SELECT
  • NM_001276346.2:c.291+355_291+356delinsCT
  • NM_001276347.2:c.317_318delinsCT
  • NP_000355.2:p.Ile116Thr
  • NP_001001430.1:p.Ile106Thr
  • NP_001001431.1:p.Ile106Thr
  • NP_001001432.1:p.Ile101Thr
  • NP_001263274.1:p.Ile116Thr
  • NP_001263276.1:p.Ile106Thr
  • LRG_431t1:c.347_348delinsCT
  • LRG_431:g.17423_17424delinsCT
  • LRG_431p1:p.Ile116Thr
  • NC_000001.10:g.201334382_201334383delinsAG
  • NM_001001430.1:c.317_318delTCinsCT
  • NM_001001430.1:c.317_318delinsCT
  • NM_001001430.2:c.317_318delTCinsCT
Protein change:
I101T
Links:
dbSNP: rs1553282523
NCBI 1000 Genomes Browser:
rs1553282523
Molecular consequence:
  • NM_001276346.2:c.291+355_291+356delinsCT - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000364.4:c.347_348delinsCT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001001430.3:c.317_318delinsCT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001001431.3:c.317_318delinsCT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001001432.3:c.302_303delinsCT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276345.2:c.347_348delinsCT - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276347.2:c.317_318delinsCT - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypertrophic cardiomyopathy 2
Synonyms:
Familial hypertrophic cardiomyopathy 2; TNNT2-Related Familial Hypertrophic Cardiomyopathy
Identifiers:
MONDO: MONDO:0007266; MedGen: C1861864; OMIM: 115195
Name:
Dilated cardiomyopathy 1D
Synonyms:
Left ventricular noncompaction 6
Identifiers:
MONDO: MONDO:0011095; MedGen: C1832243; Orphanet: 154; Orphanet: 54260; OMIM: 601494
Name:
Cardiomyopathy, familial restrictive, 3
Identifiers:
MONDO: MONDO:0012900; MedGen: C2676271; Orphanet: 75249; OMIM: 612422

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000767824Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 28, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy.

Jordan DM, Kiezun A, Baxter SM, Agarwala V, Green RC, Murray MF, Pugh T, Lebo MS, Rehm HL, Funke BH, Sunyaev SR.

Am J Hum Genet. 2011 Feb 11;88(2):183-92. doi: 10.1016/j.ajhg.2011.01.011.

PubMed [citation]
PMID:
21310275
PMCID:
PMC3035712

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, SCV000767824.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 106 of the TNNT2 protein (p.Ile106Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with TNNT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 452747). An algorithm developed specifically for the TNNT2 gene suggests that this missense change is likely to be deleterious (PMID: 21310275). 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.

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

Last Updated: Oct 26, 2024