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

ENSG00000203857 ∙ NCBI:3283 ∙ OMIM:109715 ∙ HGNC:5217 ∙ Uniprot:P14060 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HSD3B1 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	4	2	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	4	2

Variants in HSD3B1

This is a list of pathogenic ClinVar variants found in the HSD3B1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-119507502-C-G		not specified	Uncertain significance (Dec 16, 2022)
1-119507514-G-T		not specified	Uncertain significance (Mar 01, 2023)
1-119507537-C-T		not specified	Uncertain significance (Dec 11, 2023)
1-119507538-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-119507574-G-C		not specified	Uncertain significance (Jun 28, 2022)
1-119507587-G-C		not specified	Uncertain significance (Sep 30, 2021)
1-119511538-G-C		not specified	Uncertain significance (Oct 12, 2024)
1-119511567-G-C		not specified	Uncertain significance (Apr 05, 2023)
1-119511569-G-T			Likely benign (Nov 01, 2024)
1-119511583-G-A		not specified	Likely benign (Aug 08, 2023)
1-119511589-G-T		not specified	Uncertain significance (Oct 05, 2022)
1-119511592-A-G			Benign (Jul 13, 2018)
1-119511604-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-119511636-C-G		not specified	Uncertain significance (Jan 30, 2024)
1-119511661-G-A		not specified	Uncertain significance (Mar 30, 2024)
1-119513857-T-A		not specified	Uncertain significance (Sep 08, 2024)
1-119513882-T-C		not specified	Uncertain significance (Nov 15, 2024)
1-119513900-T-C		not specified	Uncertain significance (May 09, 2024)
1-119513905-G-A		not specified	Uncertain significance (Apr 24, 2024)
1-119513911-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-119513959-C-T		not specified	Uncertain significance (Aug 07, 2024)
1-119514019-G-A		not specified	Uncertain significance (Oct 29, 2024)
1-119514026-C-T		not specified	Uncertain significance (Jul 11, 2023)
1-119514052-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-119514055-G-A		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

Essentials

• essential_gene_CRISPR: N
• 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

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