4-55364153-C-CTA
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_024592.5(SRD5A3):c.445_446dupTA(p.Val150ThrfsTer9) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_024592.5 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A3 | NM_024592.5 | c.445_446dupTA | p.Val150ThrfsTer9 | frameshift_variant | Exon 3 of 5 | ENST00000264228.9 | NP_078868.1 | |
SRD5A3 | NM_001410732.1 | c.445_446dupTA | p.Val150ThrfsTer9 | frameshift_variant | Exon 3 of 4 | NP_001397661.1 | ||
SRD5A3 | XM_017008601.2 | c.310_311dupTA | p.Val105ThrfsTer9 | frameshift_variant | Exon 3 of 5 | XP_016864090.1 | ||
SRD5A3 | XM_005265767.4 | c.364+4666_364+4667dupTA | intron_variant | Intron 2 of 2 | XP_005265824.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRD5A3 | ENST00000264228.9 | c.445_446dupTA | p.Val150ThrfsTer9 | frameshift_variant | Exon 3 of 5 | 1 | NM_024592.5 | ENSP00000264228.4 | ||
ENSG00000288695 | ENST00000679707.1 | c.445_446dupTA | p.Val150ThrfsTer9 | frameshift_variant | Exon 3 of 6 | ENSP00000505713.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
SRD5A3-related disorder Pathogenic:1
The SRD5A3 c.445_446dupTA variant is predicted to result in a frameshift and premature protein termination (p.Val150Thrfs*9). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Frameshift variants in SRD5A3 are expected to be pathogenic. This variant is interpreted as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.