rs200149713
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BS1_Supporting
The NM_020433.5(JPH2):c.1894G>A(p.Glu632Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000931 in 1,610,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E632D) has been classified as Likely benign.
Frequency
Consequence
NM_020433.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JPH2 | NM_020433.5 | c.1894G>A | p.Glu632Lys | missense_variant | 4/6 | ENST00000372980.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JPH2 | ENST00000372980.4 | c.1894G>A | p.Glu632Lys | missense_variant | 4/6 | 5 | NM_020433.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000824 AC: 2AN: 242828Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131888
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1458454Hom.: 0 Cov.: 33 AF XY: 0.00000689 AC XY: 5AN XY: 725782
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | The p.Glu632Lys variant in JPH2 has not been previously reported in individuals with cardiomyopathy, but has been identified in 4/23652 African chromosomes by t he Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs200149713). Computational prediction tools and conservation analysis do not p rovide strong support for or against an impact to the protein. In summary, the c linical significance of the p.Glu632Lys variant is uncertain. - |
Hypertrophic cardiomyopathy 17;C5561970:Cardiomyopathy, dilated, 2E Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 28, 2021 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 15, 2022 | Identified in association with LVNC in published literature (Mazzarotto et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 33500567) - |
Hypertrophic cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2023 | ClinVar contains an entry for this variant (Variation ID: 504867). 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. This missense change has been observed in individual(s) with JPH2-related conditions (PMID: 33500567). This variant is present in population databases (rs200149713, gnomAD 0.02%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 632 of the JPH2 protein (p.Glu632Lys). - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2022 | The p.E632K variant (also known as c.1894G>A), located in coding exon 4 of the JPH2 gene, results from a G to A substitution at nucleotide position 1894. The glutamic acid at codon 632 is replaced by lysine, an amino acid with similar properties. This variant was described in one individual from a left ventricular non-compaction (LVNC) genetic testing cohort, who was reported to have hypertrophic cardiomyopathy (HCM) with LVNC, arrhythmias, and history of atrial septa defect; however, an additional cardiac-related variant was also detected (Mazzarotto F et al. Genet Med, 2021 05;23:856-864). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at