14-96860628-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
The NM_003384.3(VRK1):c.961C>T(p.Arg321Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000479 in 1,460,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_003384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.000195 AC: 49AN: 250920Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135638
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460922Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 726784
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Pontocerebellar hypoplasia type 1A Pathogenic:2Uncertain:1
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This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 321 of the VRK1 protein (p.Arg321Cys). This variant is present in population databases (rs772731615, gnomAD 0.1%). This missense change has been observed in individuals with VRK1-related conditions (PMID: 26583493, 31167812; internal data). ClinVar contains an entry for this variant (Variation ID: 209205). 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. Experimental studies have shown that this missense change affects VRK1 function (PMID: 31527692). For these reasons, this variant has been classified as Pathogenic. -
Pontocerebellar hypoplasia type 1A;C5882703:Neuronopathy, distal hereditary motor, autosomal recessive 10 Pathogenic:1
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Juvenile amyotrophic lateral sclerosis Pathogenic:1
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not provided Pathogenic:1
Published functional studies demonstrate a damaging effect, as the R321C variant results in reduced kinase activity (Martn-Doncel et al., 2019); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24088041, 27281532, 26583493, 31527692, 34169149, 35641352, 32298515, 32579787, 31167812) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at