HACD2

3-hydroxyacyl-CoA dehydratase 2, the group of 3-hydroxyacyl-CoA dehydratase family

Basic information

Region (hg38): 3:123490820-123585053

Previous symbols: [ "PTPLB" ]

Links

ENSG00000206527 ∙ NCBI:201562 ∙ OMIM:615939 ∙ HGNC:9640 ∙ Uniprot:Q6Y1H2 ∙ 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 HACD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HACD2 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in HACD2

This is a list of pathogenic ClinVar variants found in the HACD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-123494905-G-A		not specified	Uncertain significance (Apr 19, 2023)
3-123494913-G-T		not specified	Uncertain significance (Jul 12, 2023)
3-123528394-C-T		not specified	Uncertain significance (Aug 08, 2022)
3-123567768-C-A		not specified	Uncertain significance (Oct 25, 2022)
3-123582261-T-G		not specified	Uncertain significance (Sep 12, 2023)
3-123582280-T-C		not specified	Uncertain significance (Sep 26, 2023)
3-123582300-C-T		not specified	Uncertain significance (May 26, 2023)
3-123584976-C-A		not specified	Uncertain significance (Dec 03, 2021)
3-123585011-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-123585018-C-A		not specified	Uncertain significance (Jul 12, 2022)
3-123585020-G-A		not specified	Uncertain significance (Dec 21, 2021)
3-123585021-C-A		not specified	Uncertain significance (Dec 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HACD2	protein_coding	protein_coding	ENST00000383657	7	94366

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0703	0.918	124639	0	4	124643	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	60	117	0.514	0.00000554	1599
Missense in Polyphen		15	44.483	0.33721		579
Synonymous	0.460	42	46.0	0.914	0.00000237	497
Loss of Function	2.20	4	12.3	0.325	5.97e-7	166

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)	0.0000364	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: 0.0882

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.628
• ghis: 0.594

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hacd2

Gene ontology

• Biological process: sphingolipid biosynthetic process;fatty acid elongation;peptidyl-tyrosine dephosphorylation;long-chain fatty-acyl-CoA biosynthetic process;very long-chain fatty acid biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein tyrosine phosphatase activity;protein binding;3-hydroxyacyl-CoA dehydratase activity;enzyme binding;3R-hydroxyacyl-CoA dehydratase activity;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