rs137853168
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_001320752.2(STS):āc.1100G>Cā(p.Trp367Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000182 in 1,097,939 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W367R) has been classified as Pathogenic.
Frequency
Consequence
NM_001320752.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STS | NM_001320752.2 | c.1100G>C | p.Trp367Ser | missense_variant | 9/11 | ENST00000674429.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STS | ENST00000674429.1 | c.1100G>C | p.Trp367Ser | missense_variant | 9/11 | NM_001320752.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097939Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363333
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
X-linked ichthyosis with steryl-sulfatase deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at