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

Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000061 ( 0 hom. )

Consequence

SRD5A3
NM_024592.5 stop_gained

Scores

2
3
2

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:15

Conservation

PhyloP100: 2.80
Variant links:
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 14 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 7 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 4-55346393-G-A is Pathogenic according to our data. Variant chr4-55346393-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 96125.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-55346393-G-A is described in Lovd as [Pathogenic]. Variant chr4-55346393-G-A is described in Lovd as [Pathogenic]. Variant chr4-55346393-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SRD5A3NM_024592.5 linkc.57G>A p.Trp19* stop_gained Exon 1 of 5 ENST00000264228.9 NP_078868.1 Q9H8P0
SRD5A3NM_001410732.1 linkc.57G>A p.Trp19* stop_gained Exon 1 of 4 NP_001397661.1
SRD5A3XM_005265767.4 linkc.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
SRD5A3ENST00000264228.9 linkc.57G>A p.Trp19* stop_gained Exon 1 of 5 1 NM_024592.5 ENSP00000264228.4 Q9H8P0
ENSG00000288695ENST00000679707.1 linkc.57G>A p.Trp19* stop_gained Exon 1 of 6 ENSP00000505713.1 A0A7P0T9P9

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152140
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000118
AC:
23
AN:
195484
Hom.:
0
AF XY:
0.000193
AC XY:
21
AN XY:
108846
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000793
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000237
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000607
AC:
87
AN:
1432222
Hom.:
0
Cov.:
31
AF XY:
0.0000886
AC XY:
63
AN XY:
711210
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000919
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000455
Gnomad4 OTH exome
AF:
0.000101
GnomAD4 genome
AF:
0.0000525
AC:
8
AN:
152252
Hom.:
0
Cov.:
32
AF XY:
0.0000806
AC XY:
6
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000227
ExAC
AF:
0.000118
AC:
14

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:15
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

SRD5A3-congenital disorder of glycosylation Pathogenic:5
Nov 12, 2020
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Sep 01, 2017
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 -

Jul 15, 2017
Centre for Arab Genomic Studies, Sheikh Hamdan Award for Medical Sciences
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Lifecell International Pvt. Ltd
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

-
Neuberg Centre For Genomic Medicine, NCGM
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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
-
Genomics England Pilot Project, Genomics England
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 09, 2024
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

Oct 04, 2024
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

PVS1,PM3 (very strong),PM2 -

not provided Pathogenic:3
Jan 25, 2016
Eurofins Ntd Llc (ga)
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 14, 2023
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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) -

Jan 11, 2024
Revvity Omics, Revvity
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

SRD5A3-related disorder Pathogenic:1
Jan 01, 2024
Daryl Scott Lab, Baylor College of Medicine
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PVS1, PM2 -

Autism;C0557874:Global developmental delay;C0730290:Cone dystrophy Pathogenic:1
-
NIHR Bioresource Rare Diseases, University of Cambridge
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Congenital disorder of glycosylation Pathogenic:1
Jul 08, 2016
University of Washington Center for Mendelian Genomics, University of Washington
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Abnormality of the nervous system Pathogenic:1
Jul 10, 2021
Kariminejad - Najmabadi Pathology & Genetics Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.42
CADD
Pathogenic
37
DANN
Uncertain
0.99
Eigen
Uncertain
0.52
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Benign
0.20
N
Vest4
0.077
GERP RS
4.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs398124401; hg19: chr4-56212560; API