ABHD17A

abhydrolase domain containing 17A, depalmitoylase, the group of Depalmitoylases|Abhydrolase domain containing

Basic information

Region (hg38): 19:1876810-1885496

Previous symbols: [ "C19orf27", "FAM108A1" ]

Links

ENSG00000129968 ∙ NCBI:81926 ∙ OMIM:617942 ∙ HGNC:28756 ∙ Uniprot:Q96GS6 ∙ 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 ABHD17A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD17A 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in ABHD17A

This is a list of pathogenic ClinVar variants found in the ABHD17A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1877249-T-C		not specified	Uncertain significance (Nov 30, 2022)
19-1877264-T-C		not specified	Uncertain significance (Apr 09, 2024)
19-1877316-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-1877331-C-G		not specified	Uncertain significance (Jan 10, 2022)
19-1877611-G-C		not specified	Uncertain significance (Sep 25, 2023)
19-1877648-C-G		not specified	Uncertain significance (Oct 25, 2023)
19-1877685-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-1879927-C-T		not specified	Uncertain significance (Apr 01, 2024)
19-1879946-C-T		not specified	Uncertain significance (Mar 22, 2023)
19-1879987-G-A		not specified	Uncertain significance (May 02, 2024)
19-1880038-C-T		not specified	Uncertain significance (Jan 29, 2024)
19-1880054-T-C		not specified	Likely benign (Oct 17, 2023)
19-1880063-T-C		not specified	Uncertain significance (Jan 18, 2023)
19-1880077-A-G		not specified	Uncertain significance (Mar 01, 2023)
19-1880946-G-T		not specified	Likely benign (Feb 28, 2023)
19-1880974-G-A		not specified	Uncertain significance (Jul 13, 2022)
19-1880991-G-A		not specified	Likely benign (Oct 24, 2023)
19-1880996-G-C		not specified	Uncertain significance (Aug 10, 2021)
19-1881005-C-T		not specified	Uncertain significance (Nov 30, 2021)
19-1881326-G-C		not specified	Uncertain significance (Dec 07, 2023)
19-1881433-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-1881467-T-G		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD17A	protein_coding	protein_coding	ENST00000250974	5	8738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0189	0.963	125246	0	4	125250	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	179	245	0.731	0.0000168	2276
Missense in Polyphen		33	82.779	0.39865		809
Synonymous	0.0673	119	120	0.992	0.00000971	750
Loss of Function	2.07	5	13.1	0.382	5.60e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000188	0.0000177
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes fatty acids from S-acylated cysteine residues in proteins (PubMed:26701913). Has depalmitoylating activity towards NRAS (PubMed:26701913). Has depalmitoylating activity towards DLG4/PSD95 (PubMed:26701913). May have depalmitoylating activity towards MAP6 (By similarity). {ECO:0000250|UniProtKB:Q5XIJ5, ECO:0000269|PubMed:26701913}.

Recessive Scores

• pRec: 0.112

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.354
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abhd17a
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein depalmitoylation;protein palmitoylation;protein localization to membrane;regulation of postsynapse organization;negative regulation of protein localization to microtubule;positive regulation of protein localization to endosome
• Cellular component: plasma membrane;endosome membrane;membrane;cell junction;dendritic spine;recycling endosome membrane;glutamatergic synapse;anchored component of postsynaptic density membrane;anchored component of postsynaptic recycling endosome membrane
• Molecular function: protein binding;palmitoyl-(protein) hydrolase activity