19-49157885-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_017636.4(TRPM4):c.19G>A(p.Glu7Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000013 in 1,535,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_017636.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 31
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1382850Hom.: 0 Cov.: 33 AF XY: 0.00000147 AC XY: 1AN XY: 682378
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
TRPM4-related disorder Pathogenic:1
The TRPM4 c.19G>A variant is predicted to result in the amino acid substitution p.Glu7Lys. This variant was reported to segregate with progressive familial heart block in three branches of a large South African Afrikaner pedigree (Brink et al. 1995. PubMed ID: 7882468; Kruse et al. 2009. PubMed ID: 19726882). Functional studies showed that this variant leads to attenuated deSUMOylation, reduced endocytosis, elevated channel density at the cell surface, and altered modulation of voltage-dependent gating, suggesting a gain-of-function mechanism (Kruse et al. 2009. PubMed ID: 19726882; Hu et al. 2021. PubMed ID: 33922380). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as likely pathogenic. -
Progressive familial heart block type IB Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at