HTD2

protein-coding

hydroxyacyl-thioester dehydratase type 2

Gene summary

This gene encodes a protein that localizes to the mitochondria and can function as a 3-hydroxyacyl thioester dehydratase. This gene is located just downstream of the gene for ribonuclease P/MRP subunit p14 (RPP14) in a genomic context that is conserved among animals. The upstream RPP14 gene is thought to be co-transcribed with this gene, and bicistronic transcripts may include open reading frames for both proteins. [provided by RefSeq, May 2017]

MANE transcript

NM_001348712.2

Inheritance

—

ClinVar variants

—

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr3:58,306,262-58,320,193

External References & Databases

Ensembl (ENSG00000255154)

NCBI Gene (109703458)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HTD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001348712.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001348712.2	RefSeq	NP_001335641.1	1	MANE Select
ENST00000461393.7	Ensembl	ENSP00000484277.1	1	MANE Select
NM_001348713.1	RefSeq	NP_001335642.1	1	Standard
NM_001348714.1	RefSeq	NP_001335643.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Fatty acyl-CoA biosynthesis
Metabolism
Fatty acid metabolism
palmitate biosynthesis

Biological Process

fatty acid metabolic process
fatty-acyl-CoA biosynthetic process

Molecular Function

3-hydroxyacyl-CoA dehydratase activity

Cellular Component

nucleolus
mitochondrion
mitochondrial matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000528153
Coding exons: 1
Length: 507
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.281	75	82.2	0.913	0.00000411	1087
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mitochondrial 3-hydroxyacyl-thioester dehydratase, which may be involved in fatty acid biosynthesis. {ECO:0000269|PubMed:17898086}.;