HTD2

hydroxyacyl-thioester dehydratase type 2

Basic information

Region (hg38): 3:58306262-58320193

Links

ENSG00000255154 ∙ NCBI:109703458 ∙ ∙ HGNC:53111 ∙ Uniprot:P86397 ∙ 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 HTD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTD2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			8		1	9
Total	0	0	8	0	1

Variants in HTD2

This is a list of pathogenic ClinVar variants found in the HTD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-58310340-C-T		not specified	Uncertain significance (Jun 11, 2024)
3-58310376-C-T		not specified	Uncertain significance (Dec 16, 2023)
3-58310378-T-G		not specified	Uncertain significance (Dec 19, 2022)
3-58310381-G-A		not specified	Uncertain significance (Feb 14, 2025)
3-58310575-A-G		not specified	Uncertain significance (May 29, 2024)
3-58316507-A-G			Benign (Dec 19, 2017)
3-58316527-T-A		not specified	Uncertain significance (Feb 15, 2023)
3-58316930-G-T		not specified	Uncertain significance (Oct 04, 2024)
3-58316959-A-G		not specified	Uncertain significance (Mar 23, 2022)
3-58316964-G-A		not specified	Uncertain significance (Dec 30, 2024)
3-58316983-G-A			Benign (May 17, 2018)
3-58317473-A-G		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTD2	protein_coding	protein_coding	ENST00000528153	1	507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.221	0.657	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.281	75	82.2	0.913	0.00000411	1087
Missense in Polyphen		22	22.96	0.95818		270
Synonymous	0.975	23	29.8	0.773	0.00000146	351
Loss of Function	1.09	1	3.05	0.328	1.27e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial 3-hydroxyacyl-thioester dehydratase, which may be involved in fatty acid biosynthesis. {ECO:0000269|PubMed:17898086}.
• Pathway: Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;palmitate biosynthesis;fatty acid elongation -- saturated (Consensus)

Gene ontology

• Biological process: fatty acid metabolic process;fatty-acyl-CoA biosynthetic process
• Cellular component: nucleolus;mitochondrion;mitochondrial matrix
• Molecular function: 3-hydroxyacyl-CoA dehydratase activity