rs267606773
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001385.3(DPYS):c.1303G>A(p.Gly435Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_001385.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPYS | NM_001385.3 | c.1303G>A | p.Gly435Arg | missense_variant | 8/10 | ENST00000351513.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPYS | ENST00000351513.7 | c.1303G>A | p.Gly435Arg | missense_variant | 8/10 | 1 | NM_001385.3 | P1 | |
DPYS | ENST00000520483.5 | n.207G>A | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
DPYS | ENST00000521372.1 | n.135G>A | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
DPYS | ENST00000521601.1 | n.198-11610G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251116Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135708
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727242
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
Dihydropyrimidinase deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at