ABHD17B

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

Basic information

Region (hg38): 9:71862452-71911193

Previous symbols: [ "C9orf77", "FAM108B1" ]

Links

ENSG00000107362 ∙ NCBI:51104 ∙ OMIM:617943 ∙ HGNC:24278 ∙ Uniprot:Q5VST6 ∙ 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 ABHD17B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD17B 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in ABHD17B

This is a list of pathogenic ClinVar variants found in the ABHD17B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-71862607-C-T		not specified	Uncertain significance (Mar 01, 2023)
9-71866902-T-C		not specified	Uncertain significance (Feb 16, 2023)
9-71866908-C-T		not specified	Uncertain significance (May 12, 2024)
9-71866990-T-C		not specified	Uncertain significance (Jul 25, 2023)
9-71870173-G-C		not specified	Uncertain significance (May 31, 2023)
9-71874816-T-C		not specified	Uncertain significance (May 18, 2023)
9-71874948-G-A		not specified	Uncertain significance (Dec 16, 2023)
9-71875071-G-A		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD17B	protein_coding	protein_coding	ENST00000377041	4	48480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.254	0.740	125715	0	5	125720	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	68	162	0.420	0.00000857	1903
Missense in Polyphen		13	44.025	0.29528		549
Synonymous	-1.74	74	57.3	1.29	0.00000306	566
Loss of Function	2.39	3	11.9	0.252	6.51e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000297	0.0000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000894	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
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 DLG4/PSD95 (PubMed:26701913). Has depalmitoylating activity towards GAP43 (By similarity). Has depalmitoylating activity towards MAP6 (By similarity). Has depalmitoylating activity towards NRAS (PubMed:26701913). {ECO:0000250|UniProtKB:Q7M759, ECO:0000269|PubMed:26701913}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.547
• hipred: Y
• hipred_score: 0.728
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Abhd17b

Gene ontology

• Biological process: protein depalmitoylation;protein palmitoylation;regulation of protein localization to synapse;negative regulation of protein localization to microtubule;regulation of dendritic spine maintenance;positive regulation of protein localization to endosome
• Cellular component: 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: palmitoyl-(protein) hydrolase activity