rs121908009
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001032386.2(SUOX):c.1589G>A(p.Gly530Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,742 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_001032386.2 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 |
---|---|---|---|---|---|---|---|
SUOX | NM_001032386.2 | c.1589G>A | p.Gly530Asp | missense_variant | 5/5 | ENST00000266971.8 | |
SUOX | NM_000456.3 | c.1589G>A | p.Gly530Asp | missense_variant | 6/6 | ||
SUOX | NM_001032387.2 | c.1589G>A | p.Gly530Asp | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUOX | ENST00000266971.8 | c.1589G>A | p.Gly530Asp | missense_variant | 5/5 | 2 | NM_001032386.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251320Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135844
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461742Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727182
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Sulfite oxidase deficiency Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 26, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at