ABHD3

protein-coding

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

Gene summary

This gene encodes a protein containing an alpha/beta hydrolase fold, which is a catalytic domain found in a very wide range of enzymes. The function of this protein has not been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_138340.5

Inheritance

—

ClinVar variants

U:56B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr18:21,650,901-21,704,780

External References & Databases

Ensembl (ENSG00000158201)

Transcript & Mutation Effects

hg38 • Region Span ~53.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABHD3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138340.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			52 clinvar			52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	56	0	1	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138340.5	RefSeq	NP_612213.2	9	MANE Select
ENST00000289119.7	Ensembl	ENSP00000289119.2	9	MANE Select
NM_001308256.2	RefSeq	NP_001295185.1	7	Standard
NM_001308257.2	RefSeq	NP_001295186.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Synthesis of PC
Glycerophospholipid biosynthesis
Phospholipid metabolism

Biological Process

phosphatidylcholine biosynthetic process
cellular lipid metabolic process
phosphatidylcholine metabolic process
medium-chain fatty acid biosynthetic process
medium-chain fatty acid catabolic process

Molecular Function

phospholipase A2 activity
phospholipase A1 activity
lipase activity
short-chain carboxylesterase activity
acylglycerol lipase activity

Cellular Component

cellular_component
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000289119
Coding exons: 9
Length: 53909
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 125748
p: 0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.568	186	209	0.889	0.00000998	2633
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00019	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00059	0.00059	rare
Other	0.00050	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.829
RVIS EVS: -0.2
RVIS percentile EVS: 38.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.284

Gene Damage Prediction

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