4-55346393-G-A
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_024592.5(SRD5A3):c.57G>A(p.Trp19*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00006 in 1,584,474 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 (★★).
Frequency
Consequence
NM_024592.5 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A3 | NM_024592.5 | c.57G>A | p.Trp19* | stop_gained | Exon 1 of 5 | ENST00000264228.9 | NP_078868.1 | |
SRD5A3 | NM_001410732.1 | c.57G>A | p.Trp19* | stop_gained | Exon 1 of 4 | NP_001397661.1 | ||
SRD5A3 | XM_005265767.4 | c.57G>A | p.Trp19* | stop_gained | Exon 1 of 3 | XP_005265824.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRD5A3 | ENST00000264228.9 | c.57G>A | p.Trp19* | stop_gained | Exon 1 of 5 | 1 | NM_024592.5 | ENSP00000264228.4 | ||
ENSG00000288695 | ENST00000679707.1 | c.57G>A | p.Trp19* | stop_gained | Exon 1 of 6 | ENSP00000505713.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000118 AC: 23AN: 195484Hom.: 0 AF XY: 0.000193 AC XY: 21AN XY: 108846
GnomAD4 exome AF: 0.0000607 AC: 87AN: 1432222Hom.: 0 Cov.: 31 AF XY: 0.0000886 AC XY: 63AN XY: 711210
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74462
ClinVar
Submissions by phenotype
SRD5A3-congenital disorder of glycosylation Pathogenic:5
This sequence change creates a premature translational stop signal (p.Trp19*) in the SRD5A3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SRD5A3 are known to be pathogenic (PMID: 20637498, 20700148, 31638560). This variant is present in population databases (rs398124401, ExAC 0.1%). This variant has been observed in individual(s) with SRD5A3-congenital disorder of glycosylation (PMID: 24433453, 28940310, 20852264). ClinVar contains an entry for this variant (Variation ID: 96125). For these reasons, this variant has been classified as Pathogenic. -
This variant has been previously reported as disease-causing and was found once in our laboratory homozygous in a 5-year-old male with intellectual disability, hypotonia, ataxia, abnormal movements, dysmorphic features, microcephaly, failure to thrive, optic nerve atrophy, and a duplicated left kidney. Heterozygotes are expected to be asymptomatic carriers -
- -
A Heterozygous Nonsense variant c.57G>A in Exon 1 of the SRD5A3 gene that results in the amino acid substitution p.Trp19* was identified. The observed variant has a minimum allele frequency of 0.00012/% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic (variant ID 96125). This variant has been observed in many individuals affected with Congenital disorder of glycosylation reported by Bastaki F et al., 2018). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -
The stop gained p.W19* in SRD5A3 (NM_024592.4) has been reported in the homozygous state in affected patients(Morava et al., 2010;Gupta N et al,2018) . The variant has been classified as Pathogenic in the ClinVar database. It is observed in heterozygous state in 21/26490 (0.0793%) alleles from individuals of South Asian background in the gnomAD dataset.This variant is predicted to cause loss of normal protein function through protein truncation. For these reasons, this variant has been classified as Pathogenic. -
Kahrizi syndrome Pathogenic:3
- -
A heterozygous nonsense variant in exon 1 of the SRD5A3 gene that results in a stop codon and premature truncation of the protein at codon 19 (p.Trp19Ter) was detected. The observed variant has previously been reported in patients affected with cerebello-ocular syndrome with abnormal glycosylation [PMID: 20852264]. The p.Trp19Ter variant has a minor allele frequency of 0.03%, 0.005%, 0.01% and 0.002% in the 1000 genomes, gnomAD (v3.1), gnomdAD (v2.1) and topmed databases respectively. The in-silico prediction of the variant is damaging by MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as pathogenic. -
PVS1,PM3 (very strong),PM2 -
not provided Pathogenic:3
- -
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 29998879, 33879512, 34758253, 32581362, 24433453, 22304929, 20852264, 27480077, 28253385, 28940310, 28771251, 27457812, 25326635, 30315573, 30653986, 31980526, 31319225, 35725860) -
- -
SRD5A3-related disorder Pathogenic:1
PVS1, PM2 -
Autism;C0557874:Global developmental delay;C0730290:Cone dystrophy Pathogenic:1
- -
Congenital disorder of glycosylation Pathogenic:1
- -
Abnormality of the nervous system Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at