HSD17B1

hydroxysteroid 17-beta dehydrogenase 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 17:42552921-42555214

Previous symbols: [ "EDHB17", "EDH17B2" ]

Links

ENSG00000108786 ∙ NCBI:3292 ∙ OMIM:109684 ∙ HGNC:5210 ∙ Uniprot:P14061 ∙ 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 HSD17B1 gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSD17B1 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					1	1
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	20	1	1

Variants in HSD17B1

This is a list of pathogenic ClinVar variants found in the HSD17B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42552940-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-42552961-G-A		not specified	Uncertain significance (Sep 22, 2022)
17-42552987-C-G		not specified	Uncertain significance (May 31, 2023)
17-42552994-G-C		not specified	Likely benign (Feb 06, 2024)
17-42553159-C-G		not specified	Uncertain significance (Feb 26, 2024)
17-42553160-G-A		not specified	Likely benign (Mar 01, 2023)
17-42553196-C-A		not specified	Uncertain significance (Mar 28, 2022)
17-42553225-G-A		not specified	Uncertain significance (Feb 10, 2022)
17-42553253-C-T		not specified	Uncertain significance (Nov 08, 2022)
17-42553277-G-A		not specified	Uncertain significance (Aug 04, 2021)
17-42553483-G-C		not specified	Uncertain significance (Dec 08, 2021)
17-42553802-T-C		not specified	Uncertain significance (Mar 31, 2023)
17-42553850-G-C		not specified	Uncertain significance (Jun 13, 2023)
17-42553859-G-A		not specified	Uncertain significance (May 27, 2022)
17-42554447-G-A		not specified	Uncertain significance (Dec 07, 2021)
17-42554470-A-T		not specified	Uncertain significance (Sep 20, 2023)
17-42554496-C-T		not specified	Uncertain significance (Aug 08, 2023)
17-42554567-T-C			Benign (Jul 19, 2018)
17-42554661-C-T			Benign (May 02, 2018)
17-42554706-T-G		not specified	Uncertain significance (Nov 29, 2021)
17-42554712-A-C		not specified	Uncertain significance (Nov 02, 2023)
17-42554714-T-A		not specified	Uncertain significance (Feb 05, 2024)
17-42554745-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-42554774-A-G		not specified	Uncertain significance (Dec 28, 2023)
17-42554784-C-G		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSD17B1	protein_coding	protein_coding	ENST00000585807	6	6000

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000134	0.656	125718	0	28	125746	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.351	236	221	1.07	0.0000143	2052
Missense in Polyphen		89	83.3	1.0684		790
Synonymous	-0.878	121	109	1.11	0.00000771	733
Loss of Function	0.805	7	9.70	0.721	4.10e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000888	0.0000879
Middle Eastern	0.000165	0.000163
South Asian	0.000230	0.000229
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Favors the reduction of estrogens and androgens. Also has 20-alpha-HSD activity. Uses preferentially NADH.
• Pathway: Steroid hormone biosynthesis - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Aromatase Inhibitor Pathway (Multiple Tissues), Pharmacodynamics;Estrogen Metabolism Pathway;Aromatase Inhibitor Pathway (Breast Cell), Pharmacodynamics;Valproic Acid Pathway, Pharmacokinetics;17-Beta Hydroxysteroid Dehydrogenase III Deficiency;Androgen and Estrogen Metabolism;Aromatase deficiency;Androgen Receptor Network in Prostate Cancer;Steroid Biosynthesis;Signaling by GPCR;Signal Transduction;The canonical retinoid cycle in rods (twilight vision);G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling;estradiol biosynthesis I;superpathway of steroid hormone biosynthesis (Consensus)

Recessive Scores

• pRec: 0.285

Intolerance Scores

• loftool: 0.196
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.180
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.738

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hsd17b1
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype

Gene ontology

• Biological process: steroid biosynthetic process;estrogen biosynthetic process;estrogen metabolic process;oxidation-reduction process
• Cellular component: cytoplasm;cytosol
• Molecular function: catalytic activity;estradiol 17-beta-dehydrogenase activity;steroid binding;NADP+ binding;estradiol binding