rs397517246
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_014000.3(VCL):c.854G>A(p.Arg285His) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,614,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R285C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014000.3 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 |
---|---|---|---|---|---|---|---|
VCL | NM_014000.3 | c.854G>A | p.Arg285His | missense_variant | 7/22 | ENST00000211998.10 | |
VCL | NM_003373.4 | c.854G>A | p.Arg285His | missense_variant | 7/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCL | ENST00000211998.10 | c.854G>A | p.Arg285His | missense_variant | 7/22 | 1 | NM_014000.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251402Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135868
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727200
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74466
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 | Feb 07, 2012 | The Arg285His variant (VCL) has not been reported in the literature, but has bee n identified in one proband with HCM (this individual's son) by our laboratory. Arginine (Arg) at position 285 is not completely conserved across different spec ies, increasing the likelihood that a change would be tolerated. Computational a nalyses (biochemical amino acid properties, AlignGVGD, PolyPhen2, and SIFT) also suggest that the Arg285His variant may not impact the protein, though this info rmation is not predictive enough to rule out pathogenicity. Variants in the VCL gene have been found in individuals with HCM as well as DCM (Olson 2002, Vasile 2006). However, the number of studies is still small and the contribution of VCL to HCM and DCM, as well as the types of variants that cause disease, have not b een well established. Additional information is needed to fully assess the clini cal significance of this variant. - |
Dilated cardiomyopathy 1W Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2022 | This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 285 of the VCL protein (p.Arg285His). This variant is present in population databases (rs397517246, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with VCL-related conditions. ClinVar contains an entry for this variant (Variation ID: 45621). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available". The histidine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at