ABHD10

protein-coding

abhydrolase domain containing 10, depalmitoylase, the group of Abhydrolase domain containing

Gene summary

This gene encodes a mitochondrially-localized enzyme that acts in liver cells as a hydrolase. The encoded protein removes glucuronide from mycophenolic acid acyl-glucuronide. There is a pseudogene for this gene on chromosome 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

MANE transcript

NM_018394.4

Inheritance

—

ClinVar variants

U:53B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr3:111,979,010-111,993,368

External References & Databases

Ensembl (ENSG00000144827)

Transcript & Mutation Effects

hg38 • Region Span ~14.4 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 ABHD10 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 55

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018394.4. 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						0
missense			53 clinvar	4 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	4	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018394.4	RefSeq	NP_060864.1	5	MANE Select
ENST00000273359.8	Ensembl	ENSP00000273359.3	5	MANE Select
NM_001272069.2	RefSeq	NP_001258998.1	5	Standard
ENST00000491580.1	Ensembl	ENSP00000418162.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Glucuronidation
Phase II - Conjugation of compounds
Biological oxidations

Biological Process

glucuronoside catabolic process
cellular glucuronidation

Molecular Function

hydrolase activity, hydrolyzing O-glycosyl compounds
mycophenolic acid acyl-glucuronide esterase activity

Cellular Component

mitochondrion
mitochondrial matrix
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273359
Coding exons: 5
Length: 14354
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.233	163	172	0.950	0.00000831	1983
Missense (PolyPhen)		41	58.008	0.7068		684
Synonymous	-0.251	65	62.5	1.04	0.00000331	615
Loss of Function	1.39	10	16.0	0.626	0.00000108	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00030	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the deglucuronidation of mycophenolic acid acyl-glucuronide, a metabolite of the immunosuppressant drug mycophenolate. {ECO:0000269|PubMed:22294686}.;

Recessive Scores

pRec: 0.0996

Intolerance Scores

LoFtool: 0.702
RVIS EVS: 0.6
RVIS percentile EVS: 82.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.903

Gene Damage Prediction

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