rs762729609
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong
The NM_006295.3(VARS1):āc.1325G>Cā(p.Arg442Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,460,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R442Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_006295.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS1 | NM_006295.3 | c.1325G>C | p.Arg442Pro | missense_variant | 10/30 | ENST00000375663.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS1 | ENST00000375663.8 | c.1325G>C | p.Arg442Pro | missense_variant | 10/30 | 1 | NM_006295.3 | P1 | |
VARS1 | ENST00000489979.1 | n.636G>C | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
VARS1 | ENST00000495010.5 | n.868G>C | non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246990Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134604
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460762Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726698
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at