HSD17B12
hydroxysteroid 17-beta dehydrogenase 12, the group of Short chain dehydrogenase/reductase superfamily
Basic information
Region (hg38): 11:43680680-43856617
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
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. These statistics are base on transcript: NM_000016142.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 39 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 40 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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