ABHD4

abhydrolase domain containing 4, N-acyl phospholipase B, the group of Abhydrolase domain containing

Basic information

Region (hg38): 14:22598290-22612963

Links

ENSG00000100439 ∙ NCBI:63874 ∙ OMIM:619728 ∙ HGNC:20154 ∙ Uniprot:Q8TB40 ∙ 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 ABHD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD4 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			17
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	0	0

Variants in ABHD4

This is a list of pathogenic ClinVar variants found in the ABHD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-22601674-G-A		not specified	Uncertain significance (Sep 26, 2023)
14-22601705-G-A		not specified	Uncertain significance (Oct 31, 2023)
14-22603480-G-A		not specified	Uncertain significance (Nov 22, 2021)
14-22603486-C-T		not specified	Uncertain significance (Jul 09, 2021)
14-22603530-A-T		not specified	Uncertain significance (Mar 20, 2024)
14-22603537-A-G		not specified	Uncertain significance (Apr 04, 2024)
14-22603558-G-A		not specified	Uncertain significance (Jan 26, 2023)
14-22603696-T-C		not specified	Uncertain significance (Jun 01, 2023)
14-22603971-C-T		not specified	Uncertain significance (Dec 18, 2023)
14-22603972-C-T		not specified	Uncertain significance (Oct 17, 2023)
14-22603993-G-A		not specified	Uncertain significance (Mar 22, 2023)
14-22603998-C-T		not specified	Uncertain significance (Apr 19, 2024)
14-22604001-C-G		not specified	Uncertain significance (Aug 30, 2022)
14-22604019-G-A		not specified	Uncertain significance (Oct 10, 2023)
14-22606427-G-A		not specified	Uncertain significance (Oct 25, 2023)
14-22606470-C-A		not specified	Uncertain significance (May 21, 2024)
14-22609780-T-C		not specified	Uncertain significance (Mar 01, 2024)
14-22609789-G-A		not specified	Uncertain significance (May 26, 2022)
14-22609804-G-A		not specified	Uncertain significance (Mar 15, 2024)
14-22609861-C-T		not specified	Uncertain significance (Sep 26, 2023)
14-22610893-A-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD4	protein_coding	protein_coding	ENST00000428304	7	14120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.22e-8	0.698	125526	0	222	125748	0.000883

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.701	191	220	0.867	0.0000134	2242
Missense in Polyphen		58	63.743	0.90991		637
Synonymous	-0.827	94	84.3	1.11	0.00000519	694
Loss of Function	1.30	15	21.5	0.697	0.00000148	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000933	0.000928
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000381	0.000381
Finnish	0.00148	0.00148
European (Non-Finnish)	0.00116	0.00115
Middle Eastern	0.000381	0.000381
South Asian	0.000625	0.000621
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lysophospholipase selective for N-acyl phosphatidylethanolamine (NAPE). Contributes to the biosynthesis of N-acyl ethanolamines, including the endocannabinoid anandamide by hydrolyzing the sn-1 and sn-2 acyl chains from N-acyl phosphatidylethanolamine (NAPE) generating glycerophospho-N-acyl ethanolamine (GP-NAE), an intermediate for N-acyl ethanolamine biosynthesis. Hydrolyzes substrates bearing saturated, monounsaturated, polyunsaturated N-acyl chains. Shows no significant activity towards other lysophospholipids, including lysophosphatidylcholine, lysophosphatidylethanolamine and lysophosphatidylserine (By similarity). {ECO:0000250}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.319
• hipred: N
• hipred_score: 0.383
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.804

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Abhd4

Gene ontology

• Biological process: lipid catabolic process;phosphatidylethanolamine acyl-chain remodeling;lipid homeostasis
• Cellular component: endoplasmic reticulum membrane;lipid droplet
• Molecular function: hydrolase activity;carboxylic ester hydrolase activity