HACD4

3-hydroxyacyl-CoA dehydratase 4, the group of 3-hydroxyacyl-CoA dehydratase family

Basic information

Region (hg38): 9:20999509-21031640

Previous symbols: [ "PTPLAD2" ]

Links

ENSG00000188921 ∙ NCBI:401494 ∙ OMIM:615941 ∙ HGNC:20920 ∙ Uniprot:Q5VWC8 ∙ 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 HACD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HACD4 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in HACD4

This is a list of pathogenic ClinVar variants found in the HACD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-21007059-G-C		not specified	Uncertain significance (Feb 06, 2024)
9-21007086-T-C		not specified	Uncertain significance (May 26, 2024)
9-21007116-A-T		not specified	Uncertain significance (Sep 29, 2023)
9-21008039-G-C		not specified	Uncertain significance (Oct 27, 2022)
9-21008062-A-C		not specified	Uncertain significance (May 24, 2024)
9-21008110-G-A		not specified	Uncertain significance (Jan 24, 2024)
9-21008146-G-C		not specified	Uncertain significance (Aug 04, 2023)
9-21011610-G-A		not specified	Uncertain significance (Feb 24, 2022)
9-21011616-T-C		not specified	Uncertain significance (May 10, 2024)
9-21011634-G-C		not specified	Uncertain significance (Jan 05, 2022)
9-21015946-T-C		not specified	Uncertain significance (Aug 10, 2021)
9-21015954-T-G		not specified	Uncertain significance (Sep 10, 2024)
9-21015989-G-A		not specified	Uncertain significance (May 12, 2024)
9-21016006-G-A		not specified	Uncertain significance (Jun 16, 2023)
9-21026667-C-T		not specified	Likely benign (Dec 01, 2022)
9-21026669-G-A		not specified	Uncertain significance (May 25, 2022)
9-21026693-C-G		not specified	Uncertain significance (Jan 03, 2024)
9-21029311-G-C		not specified	Uncertain significance (Nov 15, 2024)
9-21029350-A-C		not specified	Uncertain significance (May 18, 2023)
9-21029351-C-G		not specified	Uncertain significance (Dec 19, 2022)
9-21029359-G-C		not specified	Uncertain significance (Feb 27, 2024)
9-21029367-A-T		not specified	Uncertain significance (Aug 16, 2022)
9-21031569-C-A		not specified	Uncertain significance (Jul 06, 2024)
9-21031584-G-T		not specified	Uncertain significance (Jan 31, 2023)
9-21031586-C-A		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HACD4	protein_coding	protein_coding	ENST00000495827	7	36330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000206	0.730	124722	1	52	124775	0.000212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.466	131	117	1.12	0.00000536	1505
Missense in Polyphen		46	45.188	1.018		604
Synonymous	-0.927	51	43.2	1.18	0.00000226	422
Loss of Function	1.08	9	13.2	0.681	6.40e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.00	0.00
East Asian	0.000287	0.000278
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000355	0.000344
Middle Eastern	0.000287	0.000278
South Asian	0.000104	0.0000980
Other	0.00	0.00

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. {ECO:0000269|PubMed:18554506}.
• Pathway: Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;Synthesis of very long-chain fatty acyl-CoAs (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.350
• ghis: 0.446

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hacd4

Gene ontology

• Biological process: sphingolipid biosynthetic process;fatty acid elongation;very long-chain fatty acid biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: 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