ABHD10

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

Basic information

Region (hg38): 3:111979010-111993368

Links

ENSG00000144827 ∙ NCBI:55347 ∙ OMIM:618756 ∙ HGNC:25656 ∙ Uniprot:Q9NUJ1 ∙ 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 ABHD10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD10 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			15	1		16
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	1	0

Variants in ABHD10

This is a list of pathogenic ClinVar variants found in the ABHD10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-111979086-G-T		not specified	Uncertain significance (Dec 19, 2023)
3-111979112-C-A		not specified	Likely benign (Sep 17, 2021)
3-111979140-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-111979170-C-T		not specified	Uncertain significance (Jan 31, 2024)
3-111979175-A-G		not specified	Uncertain significance (Mar 20, 2023)
3-111979192-G-A		not specified	Uncertain significance (Jun 11, 2021)
3-111979196-G-T		not specified	Uncertain significance (Jun 10, 2024)
3-111979201-C-G		not specified	Uncertain significance (Oct 03, 2022)
3-111981958-C-G		not specified	Uncertain significance (Jan 02, 2024)
3-111981963-A-G		not specified	Uncertain significance (Oct 05, 2021)
3-111986312-C-A		not specified	Uncertain significance (May 26, 2024)
3-111986924-G-A		not specified	Uncertain significance (Jun 02, 2024)
3-111986953-C-T		not specified	Uncertain significance (Jan 27, 2022)
3-111987005-C-T		not specified	Uncertain significance (Apr 29, 2024)
3-111987026-C-A		not specified	Uncertain significance (Mar 21, 2023)
3-111991384-A-T		not specified	Uncertain significance (Jan 23, 2023)
3-111991396-T-C		not specified	Uncertain significance (Oct 31, 2023)
3-111991480-A-G		not specified	Uncertain significance (Mar 29, 2024)
3-111991605-G-A		not specified	Uncertain significance (Apr 24, 2023)
3-111991633-A-T		not specified	Uncertain significance (Jan 26, 2022)
3-111991693-T-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD10	protein_coding	protein_coding	ENST00000273359	5	14354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000129	0.846	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.233	163	172	0.950	0.00000831	1983
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000298	0.000294
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the deglucuronidation of mycophenolic acid acyl-glucuronide, a metabolite of the immunosuppressant drug mycophenolate. {ECO:0000269|PubMed:22294686}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Glucuronidation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism (Consensus)

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.702
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0685
• hipred: N
• hipred_score: 0.177
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abhd10

Gene ontology

• Biological process: glucuronoside catabolic process;cellular glucuronidation
• Cellular component: mitochondrion;mitochondrial matrix;cytosol
• Molecular function: hydrolase activity, hydrolyzing O-glycosyl compounds;mycophenolic acid acyl-glucuronide esterase activity