NM_000348.4:c.586G>C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_000348.4(SRD5A2):c.586G>C(p.Gly196Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A2 | NM_000348.4 | c.586G>C | p.Gly196Arg | missense_variant | Exon 4 of 5 | ENST00000622030.2 | NP_000339.2 | |
SRD5A2 | XM_011533069.3 | c.364G>C | p.Gly122Arg | missense_variant | Exon 4 of 5 | XP_011531371.1 | ||
SRD5A2 | XM_011533072.3 | c.331G>C | p.Gly111Arg | missense_variant | Exon 6 of 7 | XP_011531374.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency Pathogenic:1
The novel mutation p.G196R and a known mutation p.Q6X were identified in a patient who had perineal hypospadias. Although in vitro studies have not been performed to investigate the functional impact of the p.G196R mutation, several lines of evidence suggest that it is a disease-causing mutation. Firstly, codon 196 is highly conserved. Secondly, in silico analysis by the PolyPhen-2 and PROVEAN software predicted p.G196R to be a "probably damaging" and "deleterious" mutation, respectively. Finally, in this same codon, pathogenic mutations G196S and G196D have been identified previously. Experiments have shown that the G196S mutation could reduce the overall enzyme activity and increase the optimum pH slightly. According to the interpretation of the American College of Medical Genetics and Genomics (ACMG) guidelines, the missense mutation p.G196R was likely to be pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at