HSD17B2

hydroxysteroid 17-beta dehydrogenase 2, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 16:82035003-82098534

Links

ENSG00000086696 ∙ NCBI:3294 ∙ OMIM:109685 ∙ HGNC:5211 ∙ Uniprot:P37059 ∙ 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 HSD17B2 gene.

• Inborn genetic diseases (27 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSD17B2 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	4	5
missense			24	3	3	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	4	7

Variants in HSD17B2

This is a list of pathogenic ClinVar variants found in the HSD17B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-82035532-C-A		not specified	Likely benign (Mar 20, 2023)
16-82035539-G-A		not specified	Uncertain significance (Apr 13, 2022)
16-82035592-G-C		not specified	Uncertain significance (Jan 31, 2022)
16-82068180-C-T		not specified	Likely benign (Jun 07, 2023)
16-82068202-A-C		not specified	Uncertain significance (Apr 22, 2022)
16-82068227-C-G		not specified	Uncertain significance (Mar 14, 2023)
16-82068227-C-T		not specified	Uncertain significance (May 11, 2022)
16-82068238-G-A		not specified	Uncertain significance (Aug 02, 2022)
16-82068265-G-A			Benign (Mar 29, 2018)
16-82068293-C-T		not specified	Uncertain significance (Jun 09, 2022)
16-82068294-G-A			Benign (Jun 26, 2018)
16-82068296-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-82068298-C-A		not specified	Uncertain significance (Feb 21, 2024)
16-82068357-G-C		not specified	Uncertain significance (Aug 13, 2021)
16-82068367-A-G		not specified	Uncertain significance (Jul 09, 2021)
16-82068369-G-A		not specified	Uncertain significance (Aug 31, 2022)
16-82070984-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-82070986-A-T		not specified	Likely benign (Oct 06, 2021)
16-82070997-G-A			Benign (Mar 05, 2018)
16-82070998-C-T		not specified	Uncertain significance (Jul 27, 2022)
16-82071059-T-C		not specified	Uncertain significance (Mar 04, 2024)
16-82071075-G-C		not specified	Uncertain significance (Jan 23, 2023)
16-82071117-C-G		not specified	Uncertain significance (Nov 18, 2023)
16-82090913-A-G			Benign (Aug 15, 2018)
16-82090925-G-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSD17B2	protein_coding	protein_coding	ENST00000199936	5	63531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.85e-10	0.0346	125541	0	207	125748	0.000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.57	279	214	1.30	0.0000113	2500
Missense in Polyphen		89	69.93	1.2727		815
Synonymous	-2.89	126	90.9	1.39	0.00000534	772
Loss of Function	-0.436	14	12.3	1.13	6.05e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000691	0.000691
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00268	0.00268
European (Non-Finnish)	0.00106	0.00106
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Capable of catalyzing the interconversion of testosterone and androstenedione, as well as estradiol and estrone. Also has 20-alpha-HSD activity. Uses NADH while EDH17B3 uses NADPH.
• Pathway: Steroid hormone biosynthesis - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Androgen Receptor Network in Prostate Cancer;Vitamin D Receptor Pathway;Steroid Biosynthesis;Metabolism of lipids;Androgen and estrogen biosynthesis and metabolism;Metabolism;Estrogen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;C21-steroid hormone biosynthesis and metabolism;Steroid hormones (Consensus)

Intolerance Scores

• loftool: 0.326
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.36

Haploinsufficiency Scores

• pHI: 0.203
• hipred: N
• hipred_score: 0.144
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsd17b2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: in utero embryonic development;placenta development;estrogen biosynthetic process;response to retinoic acid;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: estradiol 17-beta-dehydrogenase activity;17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity;testosterone dehydrogenase (NAD+) activity