HSD3B1
hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1, the group of Short chain dehydrogenase/reductase superfamily
Basic information
Region (hg38): 1:119507198-119515054
Previous symbols: [ "HSDB3", "HSD3B" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (64 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSD3B1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000862.3. 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 | 0 | |||||
| missense | 57 | 66 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 57 | 9 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HSD3B1 | protein_coding | protein_coding | ENST00000369413 | 3 | 7861 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.40e-7 | 0.292 | 125705 | 0 | 41 | 125746 | 0.000163 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.01 | 242 | 202 | 1.20 | 0.0000116 | 2415 |
| Missense in Polyphen | 74 | 57.096 | 1.2961 | 697 | ||
| Synonymous | -3.20 | 123 | 85.4 | 1.44 | 0.00000535 | 738 |
| Loss of Function | 0.415 | 11 | 12.6 | 0.874 | 8.26e-7 | 143 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000871 | 0.000870 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000150 | 0.000149 |
| Middle Eastern | 0.000871 | 0.000870 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: 3-beta-HSD is a bifunctional enzyme, that catalyzes the oxidative conversion of Delta(5)-ene-3-beta-hydroxy steroid, and the oxidative conversion of ketosteroids. The 3-beta-HSD enzymatic system plays a crucial role in the biosynthesis of all classes of hormonal steroids. Efficiently catalyzes the transformation of pregnenolone to progesterone, 17-alpha-hydroxypregnenolone to 17- alpha-hydroxyprogesterone, DHEA to 4-androstenedione, dihydrotestosterone to 5-alpha-androstane-3 beta,17 beta-diol, dehydroepiandrosterone to androstenedione and 5-alpha-androstan-3 beta,17 beta-diol to 5-alpha-dihydrotestosterone. {ECO:0000269|PubMed:1401999, ECO:0000269|PubMed:2139411}.;
- Pathway
- Cortisol synthesis and secretion - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);17-Beta Hydroxysteroid Dehydrogenase III Deficiency;Steroidogenesis;Apparent mineralocorticoid excess syndrome;3-Beta-Hydroxysteroid Dehydrogenase Deficiency;21-hydroxylase deficiency (CYP21);Corticosterone methyl oxidase I deficiency (CMO I);Corticosterone methyl oxidase II deficiency - CMO II;Adrenal Hyperplasia Type 5 or Congenital Adrenal Hyperplasia due to 17 Alpha-hydroxylase Deficiency;Adrenal Hyperplasia Type 3 or Congenital Adrenal Hyperplasia due to 21-hydroxylase Deficiency;Congenital Lipoid Adrenal Hyperplasia (CLAH) or Lipoid CAH;Androgen and Estrogen Metabolism;17-alpha-hydroxylase deficiency (CYP17);Aromatase deficiency;11-beta-hydroxylase deficiency (CYP11B1);Androgen Receptor Network in Prostate Cancer;Corticotropin-releasing hormone signaling pathway;Glucocorticoid and Mineralcorticoid Metabolism;Steroid Biosynthesis;Metabolism of lipids;Androgen and estrogen biosynthesis and metabolism;Metabolism;Mineralocorticoid biosynthesis;Androgen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Bile acid biosynthesis;C21-steroid hormone biosynthesis and metabolism;Glucocorticoid biosynthesis;androgen biosynthesis;progesterone biosynthesis;superpathway of steroid hormone biosynthesis;Steroid hormones
(Consensus)
Recessive Scores
- pRec
- 0.327
Intolerance Scores
- loftool
- 0.177
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.74
Haploinsufficiency Scores
- pHI
- 0.145
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.676
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hsd3b6
- Phenotype
Zebrafish Information Network
- Gene name
- hsd3b1
- Affected structure
- melanocyte
- Phenotype tag
- abnormal
- Phenotype quality
- dispersed
Gene ontology
- Biological process
- steroid biosynthetic process;androgen biosynthetic process;estrogen biosynthetic process;glucocorticoid biosynthetic process;mineralocorticoid biosynthetic process;C21-steroid hormone metabolic process;hippocampus development;response to corticosterone;oxidation-reduction process
- Cellular component
- mitochondrial inner membrane;mitochondrial intermembrane space;endoplasmic reticulum membrane;integral component of membrane;smooth endoplasmic reticulum membrane;intracellular membrane-bounded organelle
- Molecular function
- 3-keto sterol reductase activity;3-beta-hydroxy-delta5-steroid dehydrogenase activity;steroid delta-isomerase activity;oxidoreductase activity;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;5alpha-androstane-3beta,17beta-diol dehydrogenase activity;cholesterol dehydrogenase activity