HSD17B12

hydroxysteroid 17-beta dehydrogenase 12, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 11:43680680-43856617

Links

ENSG00000149084 ∙ NCBI:51144 ∙ OMIM:609574 ∙ HGNC:18646 ∙ Uniprot:Q53GQ0 ∙ 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 HSD17B12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSD17B12 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in HSD17B12

This is a list of pathogenic ClinVar variants found in the HSD17B12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-43680844-C-T		not specified	Uncertain significance (Mar 08, 2024)
11-43680940-G-A		not specified	Uncertain significance (Jan 17, 2024)
11-43680967-C-T		not specified	Uncertain significance (Aug 08, 2022)
11-43750955-G-A		not specified	Uncertain significance (Oct 06, 2022)
11-43754056-A-G		not specified	Likely benign (May 22, 2024)
11-43754106-G-T		not specified	Uncertain significance (Oct 30, 2023)
11-43754120-A-G		not specified	Uncertain significance (May 24, 2023)
11-43798363-T-G		not specified	Uncertain significance (Sep 17, 2021)
11-43798364-G-T		not specified	Uncertain significance (Jul 21, 2021)
11-43798398-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-43798404-C-T		not specified	Uncertain significance (Feb 15, 2023)
11-43798422-T-C		not specified	Uncertain significance (Jun 14, 2023)
11-43815444-C-A		not specified	Uncertain significance (Aug 01, 2024)
11-43815445-G-A		not specified	Uncertain significance (Oct 01, 2024)
11-43815455-C-T		not specified	Uncertain significance (Jul 02, 2024)
11-43815500-A-G		not specified	Uncertain significance (Jan 31, 2024)
11-43838364-C-G		not specified	Uncertain significance (Feb 15, 2024)
11-43840021-A-T		not specified	Uncertain significance (Jun 13, 2022)
11-43840053-G-A		not specified	Likely benign (Jun 02, 2023)
11-43854724-C-A		not specified	Uncertain significance (Apr 23, 2024)
11-43854730-T-C		not specified	Uncertain significance (Jun 07, 2024)
11-43854763-C-T		not specified	Uncertain significance (Aug 26, 2024)
11-43854785-C-T		not specified	Uncertain significance (Oct 03, 2023)
11-43854791-C-T		not specified	Uncertain significance (Aug 28, 2023)
11-43855154-T-A		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSD17B12	protein_coding	protein_coding	ENST00000278353	11	300182

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000403	0.963	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.649	147	171	0.860	0.00000849	2010
Missense in Polyphen		40	50.58	0.79083		615
Synonymous	-0.432	74	69.4	1.07	0.00000378	615
Loss of Function	1.86	8	16.0	0.499	6.74e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000111	0.000109
South Asian	0.0000666	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the second of the four reactions of the long- chain fatty acids elongation cycle. This endoplasmic reticulum- bound enzymatic process, allows the addition of two carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. This enzyme has a 3-ketoacyl-CoA reductase activity, reducing 3- ketoacyl-CoA to 3-hydroxyacyl-CoA, within each cycle of fatty acid elongation. Thereby, it may participate in the production of VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators. May also catalyze the transformation of estrone (E1) into estradiol (E2) and play a role in estrogen formation. {ECO:0000269|PubMed:12482854, ECO:0000269|PubMed:16166196}.
• Pathway: Steroid hormone biosynthesis - Homo sapiens (human);Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Metabolism of lipids;Fatty acyl-CoA biosynthesis;Glycine Serine metabolism;Androgen and estrogen biosynthesis and metabolism;Metabolism;Fatty acid metabolism;Androgen biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;C21-steroid hormone biosynthesis and metabolism;Synthesis of very long-chain fatty acyl-CoAs;Steroid hormones (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• loftool: 0.509
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.341
• ghis: 0.458

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsd17b12
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: fatty acid biosynthetic process;estrogen biosynthetic process;positive regulation of cell-substrate adhesion;extracellular matrix organization;long-chain fatty-acyl-CoA biosynthetic process;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;extracellular matrix
• Molecular function: fibronectin binding;estradiol 17-beta-dehydrogenase activity;protein binding;collagen binding;heparin binding;long-chain-3-hydroxyacyl-CoA dehydrogenase activity;3-oxo-arachidoyl-CoA reductase activity;3-oxo-behenoyl-CoA reductase activity;3-oxo-lignoceroyl-CoA reductase activity;3-oxo-cerotoyl-CoA reductase activity