4-55367628-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_024592.5(SRD5A3):c.603G>A(p.Trp201*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000248 in 1,613,996 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 Conflicting classifications of pathogenicity (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_024592.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRD5A3 | ENST00000264228.9 | c.603G>A | p.Trp201* | stop_gained | Exon 4 of 5 | 1 | NM_024592.5 | ENSP00000264228.4 | ||
ENSG00000288695 | ENST00000679707.1 | c.562+3357G>A | intron_variant | Intron 3 of 5 | ENSP00000505713.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461836Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727214
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
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Congenital disorder of glycosylation Pathogenic:1
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not provided Pathogenic:1
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SRD5A3-congenital disorder of glycosylation Uncertain:1
The SRD5A3 c.603G>A (p.Trp201Ter) variant is a stop-gained variant predicted to result in premature termination of the protein. The p.Trp201Ter variant has been reported in one study in which it was identified in a homozygous state in two siblings with congenital disorders of glycosylation (Wheeler et al. 2016). Both siblings have a severe phenotype with some features in common, including skin abnormalities, unusual sacral lesions, impaired psychomotor development, mild hypotonia and ataxia, febrile seizures, and differing dysmorphic features. Control data are unavailable for this variant, which is not found in the 1000 Genomes Project, the Exome Sequencing Project, the Exome Aggregation Consortium, or the Genome Aggregation Database despite being located in areas of good sequence coverage, so the variant is presumed rare. Based on the limited evidence and the potential impact of stop-gained variants, the p.Trp201Ter variant is classified as a variant of uncertain significance but suspicious for congenital disorders of glycosylation. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at