rs727504488

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP5

The NM_001276345.2(TNNT2):​c.784G>A​(p.Glu262Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

TNNT2
NM_001276345.2 missense

Scores

3
12
5

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:1

Conservation

PhyloP100: 2.98
Variant links:
Genes affected
TNNT2 (HGNC:11949): (troponin T2, cardiac type) This gene encodes the cardiac isoform of troponin T. The encoded protein is the tropomyosin-binding subunit of the troponin complex, which is located on the thin filament of striated muscles and regulates muscle contraction in response to alterations in intracellular calcium ion concentration. Mutations in this gene have been associated with familial hypertrophic cardiomyopathy as well as with dilated cardiomyopathy. [provided by RefSeq, May 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM1
In a chain Troponin T, cardiac muscle (size 296) in uniprot entity TNNT2_HUMAN there are 88 pathogenic changes around while only 9 benign (91%) in NM_001276345.2
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-201361305-C-T is Pathogenic according to our data. Variant chr1-201361305-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 178850.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNNT2NM_001276345.2 linkuse as main transcriptc.784G>A p.Glu262Lys missense_variant 15/17 ENST00000656932.1 NP_001263274.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNNT2ENST00000656932.1 linkuse as main transcriptc.784G>A p.Glu262Lys missense_variant 15/17 NM_001276345.2 ENSP00000499593 A2P45379-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Primary familial dilated cardiomyopathy Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingMolecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart InstituteApr 28, 2017- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineSep 24, 2013The Glu252Lys variant in TNNT2 has now been identified by our laboratory in 2 Ca ucasian individuals with DCM and segregated with disease in 1 affected relative. It has not been identified in large population studies. Computational analyses (biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT ) suggest that the Glu252Lys variant may not impact the protein, though this inf ormation is not predictive enough to rule out pathogenicity. Additional informat ion is needed to fully assess the clinical significance of this variant. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.76
CardioboostCm
Benign
0.041
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.030
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.83
.;.;.;.;D;.;.;.;.;.;D
Eigen
Benign
-0.020
Eigen_PC
Benign
0.063
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.95
.;D;D;D;D;D;D;.;.;D;.
M_CAP
Pathogenic
0.43
D
MetaRNN
Uncertain
0.62
D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
0.17
D
MutationAssessor
Benign
1.8
.;.;.;.;L;.;.;.;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.59
T
PROVEAN
Uncertain
-2.4
N;N;D;.;.;.;.;.;D;N;N
REVEL
Uncertain
0.63
Sift
Uncertain
0.021
D;D;D;.;.;.;.;.;D;D;D
Sift4G
Uncertain
0.035
D;D;D;T;D;T;D;T;T;D;.
Polyphen
0.073
.;.;.;.;B;.;.;.;.;.;.
Vest4
0.51
MutPred
0.41
.;.;.;.;Gain of MoRF binding (P = 0.0081);.;.;.;.;.;.;
MVP
0.90
MPC
0.91
ClinPred
0.88
D
GERP RS
3.7
Varity_R
0.58
gMVP
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs727504488; hg19: chr1-201330433; API