ABHD3

abhydrolase domain containing 3, phospholipase, the group of Abhydrolase domain containing

Basic information

Region (hg38): 18:21650901-21704780

Links

ENSG00000158201 ∙ NCBI:171586 ∙ OMIM:612197 ∙ HGNC:18718 ∙ Uniprot:Q8WU67 ∙ 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 ABHD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD3 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					1	1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	1

Variants in ABHD3

This is a list of pathogenic ClinVar variants found in the ABHD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-21651601-T-A		not specified	Uncertain significance (Mar 21, 2022)
18-21651652-A-G		not specified	Uncertain significance (Dec 13, 2022)
18-21651709-G-C		not specified	Uncertain significance (Aug 30, 2022)
18-21657019-G-C		not specified	Uncertain significance (Mar 29, 2022)
18-21659193-G-A			Benign (May 08, 2018)
18-21659273-C-T		not specified	Uncertain significance (Feb 21, 2024)
18-21659302-G-A		not specified	Uncertain significance (Dec 03, 2021)
18-21659314-A-G		not specified	Uncertain significance (Oct 12, 2022)
18-21659315-T-A		not specified	Uncertain significance (Apr 24, 2023)
18-21664158-G-A		not specified	Uncertain significance (Jan 09, 2024)
18-21664227-G-T		not specified	Uncertain significance (Nov 15, 2021)
18-21683945-C-T		not specified	Uncertain significance (Feb 23, 2023)
18-21702399-G-C		not specified	Uncertain significance (Mar 19, 2024)
18-21702449-C-T		not specified	Uncertain significance (Oct 17, 2023)
18-21703599-G-A		not specified	Uncertain significance (May 18, 2023)
18-21703660-C-T		not specified	Uncertain significance (Feb 17, 2022)
18-21703697-G-T		not specified	Uncertain significance (May 10, 2024)
18-21703719-C-T		not specified	Uncertain significance (Aug 30, 2022)
18-21704550-C-T		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD3	protein_coding	protein_coding	ENST00000289119	9	53909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-9	0.390	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.568	186	209	0.889	0.00000998	2633
Missense in Polyphen		52	69.214	0.75129		862
Synonymous	0.760	72	80.7	0.892	0.00000408	792
Loss of Function	0.935	16	20.6	0.777	0.00000103	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000371	0.000371
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000356	0.000352
Middle Eastern	0.000329	0.000326
South Asian	0.000594	0.000588
Other	0.000496	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phospholipase that may play a role in phospholipids remodeling. May selectively cleave myristate (C14)-containing phosphatidylcholines through its predominant phospholipase 1 activity, cleaving preferentially acyl groups in sn1 position. In parallel, may have a minor phospholipase 2 activity acting on acyl groups in position sn2. In addition to (C14)-containing phosphatidylcholines, may also act on other medium-chain- containing and oxidatively truncated phospholipids. {ECO:0000269|PubMed:21926997}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PC;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.829
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.576
• hipred: N
• hipred_score: 0.350
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.284

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abhd3

Gene ontology

• Biological process: phosphatidylcholine biosynthetic process;cellular lipid metabolic process;phosphatidylcholine metabolic process;medium-chain fatty acid biosynthetic process;medium-chain fatty acid catabolic process
• Cellular component: cellular_component;plasma membrane;integral component of membrane
• Molecular function: phospholipase A2 activity;phospholipase A1 activity;lipase activity;short-chain carboxylesterase activity;acylglycerol lipase activity;phosphatidylserine 1-acylhydrolase activity;1-acyl-2-lysophosphatidylserine acylhydrolase activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)