ACAP1

ArfGAP with coiled-coil, ankyrin repeat and PH domains 1, the group of Ankyrin repeat domain containing|BAR-PH domain containing|ArfGAPs

Basic information

Region (hg38): 17:7336529-7351477

Previous symbols: [ "CENTB1" ]

Links

ENSG00000072818 ∙ NCBI:9744 ∙ OMIM:607763 ∙ HGNC:16467 ∙ Uniprot:Q15027 ∙ 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 ACAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACAP1 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			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	0	0

Variants in ACAP1

This is a list of pathogenic ClinVar variants found in the ACAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7336738-A-G		not specified	Uncertain significance (Sep 17, 2021)
17-7336738-A-T		not specified	Uncertain significance (Jan 27, 2022)
17-7336747-C-G		not specified	Uncertain significance (Aug 14, 2023)
17-7336781-G-A		not specified	Uncertain significance (Jun 04, 2024)
17-7341948-C-G		not specified	Uncertain significance (Mar 16, 2022)
17-7341984-C-T		not specified	Uncertain significance (Feb 27, 2024)
17-7341996-G-A		not specified	Uncertain significance (Mar 29, 2024)
17-7342009-C-A		not specified	Uncertain significance (Sep 26, 2023)
17-7342024-T-C		not specified	Uncertain significance (Apr 19, 2024)
17-7342064-G-A		not specified	Uncertain significance (Apr 27, 2023)
17-7342308-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-7342467-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-7343386-C-G		not specified	Uncertain significance (Jan 04, 2024)
17-7343408-G-T		not specified	Uncertain significance (Feb 10, 2022)
17-7343473-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-7343868-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-7343920-C-G		not specified	Uncertain significance (Dec 02, 2022)
17-7343949-G-C		not specified	Uncertain significance (May 24, 2023)
17-7344088-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-7344554-G-A		not specified	Uncertain significance (Mar 21, 2023)
17-7344627-A-G		not specified	Uncertain significance (Aug 13, 2021)
17-7346872-A-T		not specified	Uncertain significance (Dec 26, 2023)
17-7346899-C-T		not specified	Uncertain significance (Nov 09, 2023)
17-7347104-G-C		not specified	Uncertain significance (Mar 04, 2024)
17-7347104-G-T		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACAP1	protein_coding	protein_coding	ENST00000158762	22	14950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0676	0.932	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	311	448	0.695	0.0000264	4736
Missense in Polyphen		73	153.66	0.47508		1655
Synonymous	1.53	147	173	0.852	0.00000970	1522
Loss of Function	4.53	11	43.0	0.256	0.00000227	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000349
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000102	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6) required for clathrin-dependent export of proteins from recycling endosomes to trans-Golgi network and cell surface. Required for regulated export of ITGB1 from recycling endosomes to the cell surface and ITGB1-dependent cell migration. {ECO:0000269|PubMed:11062263, ECO:0000269|PubMed:16256741, ECO:0000269|PubMed:17398097, ECO:0000269|PubMed:17664335, ECO:0000269|PubMed:22645133}.
• Pathway: Endocytosis - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway;Arf6 trafficking events;Arf6 signaling events (Consensus)

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• loftool: 0.706
• rvis_EVS: 0
• rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

• pHI: 0.632
• hipred: Y
• hipred_score: 0.651
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.549

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acap1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein transport;positive regulation of GTPase activity
• Cellular component: membrane;recycling endosome membrane
• Molecular function: GTPase activator activity;protein binding;metal ion binding