rs772283403
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PP3PP5_Very_Strong
The NM_000348.4(SRD5A2):c.704A>T(p.Tyr235Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000101 in 1,577,648 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_000348.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A2 | NM_000348.4 | c.704A>T | p.Tyr235Phe | missense_variant | Exon 5 of 5 | ENST00000622030.2 | NP_000339.2 | |
SRD5A2 | XM_011533069.3 | c.482A>T | p.Tyr161Phe | missense_variant | Exon 5 of 5 | XP_011531371.1 | ||
SRD5A2 | XM_011533072.3 | c.449A>T | p.Tyr150Phe | missense_variant | Exon 7 of 7 | XP_011531374.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000982 AC: 14AN: 1425548Hom.: 0 Cov.: 28 AF XY: 0.00000849 AC XY: 6AN XY: 706398
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency Pathogenic:2
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The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SRD5A2 protein function. ClinVar contains an entry for this variant (Variation ID: 459644). This missense change has been observed in individual(s) with steroid 5-alpha-reductase 2 deficiency (PMID: 8110760, 12699446, 16181229, 17609295, 21147889, 25266188, 27070133). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 235 of the SRD5A2 protein (p.Tyr235Phe). -
See cases Pathogenic:1
ACMG categories: PS1,PS4,PP5,BP1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at