rs587776521
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_024592.5(SRD5A3):c.286_288delinsTGAGTAAGGC(p.Gln96Ter) variant causes a stop gained, frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
SRD5A3
NM_024592.5 stop_gained, frameshift
NM_024592.5 stop_gained, frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.83
Genes affected
SRD5A3 (HGNC:25812): (steroid 5 alpha-reductase 3) The protein encoded by this gene belongs to the steroid 5-alpha reductase family, and polyprenol reductase subfamily. It is involved in the production of androgen 5-alpha-dihydrotestosterone (DHT) from testosterone, and maintenance of the androgen-androgen receptor activation pathway. This protein is also necessary for the conversion of polyprenol into dolichol, which is required for the synthesis of dolichol-linked monosaccharides and the oligosaccharide precursor used for N-linked glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type Iq. [provided by RefSeq, Mar 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 4-55359410-CAA-TGAGTAAGGC is Pathogenic according to our data. Variant chr4-55359410-CAA-TGAGTAAGGC is described in ClinVar as [Pathogenic]. Clinvar id is 18404.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A3 | NM_024592.5 | c.286_288delinsTGAGTAAGGC | p.Gln96Ter | stop_gained, frameshift_variant | 2/5 | ENST00000264228.9 | |
SRD5A3 | NM_001410732.1 | c.286_288delinsTGAGTAAGGC | p.Gln96Ter | stop_gained, frameshift_variant | 2/4 | ||
SRD5A3 | XM_005265767.4 | c.286_288delinsTGAGTAAGGC | p.Gln96Ter | stop_gained, frameshift_variant | 2/3 | ||
SRD5A3 | XM_017008601.2 | c.151_153delinsTGAGTAAGGC | p.Gln51Ter | stop_gained, frameshift_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A3 | ENST00000264228.9 | c.286_288delinsTGAGTAAGGC | p.Gln96Ter | stop_gained, frameshift_variant | 2/5 | 1 | NM_024592.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SRD5A3-congenital disorder of glycosylation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 23, 2010 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at