12-56002258-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001032386.2(SUOX):c.37C>T(p.Gln13*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Q13Q) has been classified as Likely benign.
Frequency
Consequence
NM_001032386.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUOX | NM_001032386.2 | c.37C>T | p.Gln13* | stop_gained | Exon 3 of 5 | ENST00000266971.8 | NP_001027558.1 | |
SUOX | NM_000456.3 | c.37C>T | p.Gln13* | stop_gained | Exon 4 of 6 | NP_000447.2 | ||
SUOX | NM_001032387.2 | c.37C>T | p.Gln13* | stop_gained | Exon 2 of 4 | NP_001027559.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459976Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726414
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
Sulfite oxidase deficiency Pathogenic:1
This sequence change creates a premature translational stop signal (p.Gln13*) in the SUOX gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SUOX are known to be pathogenic (PMID: 1212661, 9600976, 15952210, 32978145). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SUOX-related conditions. For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at