ABHD17C

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

Basic information

Region (hg38): 15:80679684-80755621

Previous symbols: [ "FAM108C1" ]

Links

ENSG00000136379 ∙ NCBI:58489 ∙ OMIM:617944 ∙ HGNC:26925 ∙ Uniprot:Q6PCB6 ∙ 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 ABHD17C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD17C 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in ABHD17C

This is a list of pathogenic ClinVar variants found in the ABHD17C region.

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

Position	Type	Phenotype	Significance	ClinVar
15-80695509-G-C		not specified	Uncertain significance (Jun 01, 2023)
15-80695568-C-G		not specified	Uncertain significance (Jan 08, 2024)
15-80695589-G-A		not specified	Uncertain significance (Sep 18, 2023)
15-80695604-C-T		not specified	Uncertain significance (Aug 17, 2022)
15-80695608-C-T		not specified	Uncertain significance (Apr 13, 2022)
15-80695614-C-G		not specified	Uncertain significance (Oct 12, 2021)
15-80695773-C-T		not specified	Uncertain significance (Jan 03, 2024)
15-80695785-G-C		not specified	Uncertain significance (Oct 12, 2021)
15-80695956-G-A		not specified	Uncertain significance (Jul 20, 2021)
15-80696007-C-A		not specified	Uncertain significance (Oct 18, 2021)
15-80749520-G-A		not specified	Uncertain significance (Nov 17, 2022)
15-80754258-G-A		not specified	Uncertain significance (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD17C	protein_coding	protein_coding	ENST00000258884	3	75938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.958	0.0423	115041	0	1	115042	0.00000435

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.14	52	166	0.314	0.00000872	2081
Missense in Polyphen		7	58.042	0.1206		690
Synonymous	0.337	68	71.6	0.949	0.00000421	670
Loss of Function	2.91	0	9.89	0.00	5.09e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000295	0.0000295
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
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. Has depalmitoylating activity towards NRAS and DLG4/PSD95. {ECO:0000269|PubMed:26701913}.

Recessive Scores

• pRec: 0.104

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.727
• ghis: 0.585

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abhd17c

Gene ontology

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