HSD17B13

hydroxysteroid 17-beta dehydrogenase 13, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 4:87303789-87322886

Links

ENSG00000170509 ∙ NCBI:345275 ∙ OMIM:612127 ∙ HGNC:18685 ∙ Uniprot:Q7Z5P4 ∙ 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 HSD17B13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSD17B13 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			23	1	4	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region					1	1
non coding						0
Total	0	0	23	1	6

Variants in HSD17B13

This is a list of pathogenic ClinVar variants found in the HSD17B13 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-87305247-C-T		not specified	Uncertain significance (Dec 21, 2023)
4-87305258-T-A		not specified	Uncertain significance (May 12, 2024)
4-87305274-G-A		not specified	Uncertain significance (Aug 12, 2021)
4-87305285-G-A			Benign (May 18, 2018)
4-87305295-G-T		not specified	Uncertain significance (Oct 16, 2024)
4-87310240-T-TA		HSD17B13 POLYMORPHISM • FATTY LIVER DISEASE, PROTECTION AGAINST	Benign (Jul 13, 2018)
4-87310247-G-T		not specified	Likely benign (Dec 19, 2022)
4-87310264-T-C		not specified	Uncertain significance (Aug 11, 2022)
4-87310276-G-T			Benign (May 18, 2018)
4-87310277-G-A			Benign (Oct 29, 2020)
4-87310294-T-C		not specified	Uncertain significance (Nov 28, 2024)
4-87310339-G-A			Benign (May 18, 2018)
4-87313835-T-C		not specified	Uncertain significance (Oct 25, 2023)
4-87313856-A-C		not specified	Uncertain significance (Jun 07, 2024)
4-87313905-C-T		not specified	Uncertain significance (Oct 20, 2024)
4-87313925-C-T		not specified	Uncertain significance (May 08, 2023)
4-87313946-G-A		not specified	Uncertain significance (May 16, 2024)
4-87315502-A-T		not specified	Uncertain significance (Mar 02, 2023)
4-87315518-C-T		not specified	Uncertain significance (Aug 02, 2022)
4-87315549-G-A			Benign (Jun 01, 2024)
4-87315607-A-C			Benign (Dec 31, 2019)
4-87317160-C-T		not specified	Uncertain significance (Oct 09, 2024)
4-87317181-C-T		not specified	Uncertain significance (Jun 24, 2022)
4-87317193-C-T		not specified	Uncertain significance (Jul 17, 2024)
4-87318336-A-G		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSD17B13	protein_coding	protein_coding	ENST00000328546	7	19118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000274	0.785	122064	263	3420	125747	0.0148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0219	166	167	0.995	0.00000910	1947
Missense in Polyphen		44	44.14	0.99684		586
Synonymous	0.518	59	64.3	0.918	0.00000392	594
Loss of Function	1.20	9	13.8	0.653	7.65e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.226	0.187
Ashkenazi Jewish	0.00233	0.00218
East Asian	0.0000544	0.0000544
Finnish	0.0116	0.0115
European (Non-Finnish)	0.00369	0.00359
Middle Eastern	0.0000544	0.0000544
South Asian	0.000614	0.000588
Other	0.0116	0.0101

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of lipids;Metabolism;Lipid particle organization (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.208
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0313

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsd17b13
• Phenotype: normal phenotype

Gene ontology

• Biological process: biological_process;lipid droplet organization;positive regulation of lipid biosynthetic process;oxidation-reduction process
• Cellular component: cellular_component;extracellular region;lipid droplet;cytosol
• Molecular function: molecular_function;steroid dehydrogenase activity