ABHD2

abhydrolase domain containing 2, acylglycerol lipase, the group of Abhydrolase domain containing

Basic information

Region (hg38): 15:89087459-89202355

Links

ENSG00000140526 ∙ NCBI:11057 ∙ OMIM:612196 ∙ HGNC:18717 ∙ Uniprot:P08910 ∙ 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 ABHD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD2 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					3	3
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	15	0	4

Variants in ABHD2

This is a list of pathogenic ClinVar variants found in the ABHD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-89116349-C-T		not specified	Uncertain significance (Mar 16, 2022)
15-89116364-G-A		not specified	Uncertain significance (Jun 01, 2023)
15-89116376-G-A		not specified	Uncertain significance (Sep 30, 2024)
15-89116506-C-G		not specified	Uncertain significance (Jan 10, 2023)
15-89155379-T-C		not specified	Uncertain significance (Jul 05, 2024)
15-89155423-A-G		not specified	Uncertain significance (Oct 08, 2024)
15-89175880-G-A		not specified	Uncertain significance (Jul 20, 2021)
15-89175938-C-G		not specified	Uncertain significance (Feb 27, 2024)
15-89175964-G-A		not specified	Uncertain significance (Jan 03, 2024)
15-89188255-G-A		not specified	Uncertain significance (Aug 22, 2022)
15-89188294-A-G		not specified	Uncertain significance (May 02, 2024)
15-89188312-G-T			Benign (May 08, 2018)
15-89191089-C-T			Benign (May 23, 2018)
15-89191132-A-G		not specified	Uncertain significance (Dec 26, 2023)
15-89191136-G-A		not specified	Uncertain significance (Jan 10, 2022)
15-89193239-A-G		not specified	Uncertain significance (Mar 01, 2023)
15-89193290-G-A		not specified	Uncertain significance (Dec 09, 2023)
15-89195233-G-A		not specified	Uncertain significance (May 27, 2022)
15-89195241-G-A		not specified	Uncertain significance (Jun 02, 2024)
15-89195345-C-T			Benign (May 23, 2018)
15-89195355-A-G		not specified	Uncertain significance (Apr 01, 2024)
15-89195405-G-A			Benign (May 09, 2018)
15-89195412-G-A		not specified	Uncertain significance (Aug 21, 2023)
15-89195415-C-A		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD2	protein_coding	protein_coding	ENST00000352732	9	114902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.682	0.318	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	161	262	0.613	0.0000156	2798
Missense in Polyphen		24	73.467	0.32668		770
Synonymous	-0.526	112	105	1.07	0.00000669	812
Loss of Function	3.46	4	21.2	0.188	9.98e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Progesterone-dependent acylglycerol lipase that catalyzes hydrolysis of endocannabinoid arachidonoylglycerol (AG) from cell membrane (PubMed:26989199). Acts as a progesterone receptor: progesterone-binding activates the acylglycerol lipase activity, mediating degradation of 1-arachidonoylglycerol (1AG) and 2-arachidonoylglycerol (2AG) to glycerol and arachidonic acid (AA) (PubMed:26989199). Plays a key role in sperm capacitation in response to progesterone by mediating degradation of 2AG, an inhibitor of the sperm calcium channel CatSper, leading to calcium influx via CatSper and sperm activation (PubMed:26989199). May also play a role in smooth muscle cells migration (By similarity). {ECO:0000250|UniProtKB:Q9QXM0, ECO:0000269|PubMed:26989199}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.419
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.192
• hipred: Y
• hipred_score: 0.662
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abhd2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: acrosome reaction;response to wounding;negative regulation of cell migration;response to progesterone;steroid hormone mediated signaling pathway;cellular lipid metabolic process;acylglycerol catabolic process;sperm capacitation;medium-chain fatty acid biosynthetic process;medium-chain fatty acid catabolic process
• Cellular component: acrosomal vesicle;integral component of membrane;sperm flagellum;sperm plasma membrane
• Molecular function: steroid hormone receptor activity;lipase activity;short-chain carboxylesterase activity;hormone binding;acylglycerol lipase activity