HACD3

3-hydroxyacyl-CoA dehydratase 3, the group of 3-hydroxyacyl-CoA dehydratase family

Basic information

Region (hg38): 15:65530418-65578349

Previous symbols: [ "PTPLAD1" ]

Links

ENSG00000074696 ∙ NCBI:51495 ∙ OMIM:615940 ∙ HGNC:24175 ∙ Uniprot:Q9P035 ∙ 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 HACD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HACD3 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in HACD3

This is a list of pathogenic ClinVar variants found in the HACD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65551703-G-A		not specified	Uncertain significance (Feb 25, 2025)
15-65556749-A-G		not specified	Uncertain significance (Nov 08, 2024)
15-65556815-C-T		not specified	Uncertain significance (Apr 08, 2024)
15-65556830-G-A		not specified	Uncertain significance (Sep 02, 2024)
15-65556860-G-A		not specified	Uncertain significance (Jun 17, 2024)
15-65556872-A-T		not specified	Uncertain significance (Oct 25, 2024)
15-65556881-C-T		not specified	Uncertain significance (Jan 07, 2025)
15-65556888-G-A		not specified	Uncertain significance (Dec 01, 2022)
15-65556889-G-A		not specified	Uncertain significance (Jan 07, 2025)
15-65558690-G-A		not specified	Uncertain significance (Jul 16, 2024)
15-65558692-C-A		not specified	Uncertain significance (Mar 01, 2025)
15-65558696-A-G		not specified	Uncertain significance (Apr 18, 2024)
15-65558715-C-A		not specified	Uncertain significance (Jul 27, 2024)
15-65558720-G-T		not specified	Uncertain significance (Jan 11, 2023)
15-65562841-G-C		not specified	Uncertain significance (Feb 07, 2023)
15-65564269-T-C		not specified	Uncertain significance (Dec 25, 2024)
15-65564287-C-T		not specified	Uncertain significance (Feb 28, 2024)
15-65564314-C-T		not specified	Uncertain significance (Jan 29, 2025)
15-65570146-A-G		not specified	Uncertain significance (Jan 16, 2024)
15-65570160-G-T		not specified	Uncertain significance (Feb 14, 2023)
15-65570181-T-C		not specified	Uncertain significance (Sep 14, 2023)
15-65571616-T-C		not specified	Uncertain significance (Nov 15, 2024)
15-65572241-C-T		not specified	Uncertain significance (Dec 13, 2023)
15-65572255-A-C		not specified	Uncertain significance (Aug 21, 2023)
15-65572268-A-G		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HACD3	protein_coding	protein_coding	ENST00000261875	11	47932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00930	0.990	124620	0	33	124653	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	153	193	0.792	0.0000102	2367
Missense in Polyphen		52	73.829	0.70433		922
Synonymous	1.60	51	67.7	0.753	0.00000354	653
Loss of Function	3.07	8	24.3	0.329	0.00000138	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000165	0.000158
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.000335	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.000196	0.000195
Middle Eastern	0.000335	0.000334
South Asian	0.00	0.00
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the third 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 catalyzes the dehydration of the 3-hydroxyacyl-CoA intermediate into trans-2,3-enoyl-CoA, within each cycle of fatty acid elongation. Thereby, it participates 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 be involved in Rac1-signaling pathways leading to the modulation of gene expression. Promotes insulin receptor/INSR autophosphorylation and is involved in INSR internalization (PubMed:25687571). {ECO:0000269|PubMed:10747961, ECO:0000269|PubMed:18554506, ECO:0000269|PubMed:25687571}.
• Pathway: 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;Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;Synthesis of very long-chain fatty acyl-CoAs (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.595
• ghis: 0.612

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hacd3

Gene ontology

• Biological process: I-kappaB kinase/NF-kappaB signaling;activation of JUN kinase activity;small GTPase mediated signal transduction;Rho protein signal transduction;Rac protein signal transduction;sphingolipid biosynthetic process;fatty acid elongation;very long-chain fatty acid biosynthetic process;positive regulation of GTPase activity;positive regulation of viral genome replication;positive regulation by virus of viral protein levels in host cell
• Cellular component: mitochondrion;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;focal adhesion;integral component of membrane;nuclear membrane
• Molecular function: GTPase activator activity;protein binding;3-hydroxyacyl-CoA dehydratase activity;enzyme binding;very-long-chain 3-hydroxyacyl-CoA dehydratase activity;3-hydroxy-arachidoyl-CoA dehydratase activity;3-hydroxy-behenoyl-CoA dehydratase activity;3-hydroxy-lignoceroyl-CoA dehydratase activity