SRD5A1
steroid 5 alpha-reductase 1, the group of Steroid 5-alpha reductase family
Basic information
Region (hg38): 5:6633290-6676539
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (32 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRD5A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001047.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 30 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 3 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SRD5A1 | protein_coding | protein_coding | ENST00000274192 | 5 | 36220 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000116 | 0.606 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.590 | 129 | 149 | 0.864 | 0.00000748 | 1653 |
| Missense in Polyphen | 39 | 51.169 | 0.76217 | 620 | ||
| Synonymous | -1.09 | 71 | 60.2 | 1.18 | 0.00000312 | 505 |
| Loss of Function | 0.844 | 9 | 12.2 | 0.739 | 6.08e-7 | 130 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000602 | 0.0000602 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000947 | 0.0000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000164 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Converts testosterone into 5-alpha-dihydrotestosterone and progesterone or corticosterone into their corresponding 5- alpha-3-oxosteroids. It plays a central role in sexual differentiation and androgen physiology.;
- Pathway
- Steroid hormone biosynthesis - Homo sapiens (human);17-Beta Hydroxysteroid Dehydrogenase III Deficiency;Androgen and Estrogen Metabolism;Aromatase deficiency;Metabolism of lipids;Androgen and estrogen biosynthesis and metabolism;Metabolism;allopregnanolone biosynthesis;Androgen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Bile acid biosynthesis;androgen biosynthesis;superpathway of steroid hormone biosynthesis;Steroid hormones
(Consensus)
Intolerance Scores
- loftool
- 0.612
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.0587
- hipred
- N
- hipred_score
- 0.271
- ghis
- 0.503
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.954
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Srd5a1
- Phenotype
- endocrine/exocrine gland phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- urogenital system development;liver development;steroid biosynthetic process;androgen biosynthetic process;androgen catabolic process;sex determination;male gonad development;cellular response to starvation;response to muscle activity;diterpenoid metabolic process;spinal cord development;hippocampus development;thalamus development;hypothalamus development;pituitary gland development;cerebral cortex development;electron transport chain;cell differentiation;male genitalia development;female genitalia development;response to follicle-stimulating hormone;cellular response to insulin stimulus;serotonin metabolic process;progesterone metabolic process;circadian sleep/wake cycle, REM sleep;response to estrogen;bone development;response to growth hormone;response to fungicide;cellular response to cAMP;cellular response to growth factor stimulus;cellular response to estradiol stimulus;cellular response to testosterone stimulus;cellular response to dexamethasone stimulus;cellular response to epinephrine stimulus
- Cellular component
- endoplasmic reticulum membrane;integral component of membrane;organelle membrane;neuronal cell body;myelin sheath;perinuclear region of cytoplasm;cell body fiber
- Molecular function
- 3-oxo-5-alpha-steroid 4-dehydrogenase activity;electron transfer activity;oxidoreductase activity;amide binding;cholestenone 5-alpha-reductase activity;NADPH binding