ACAP2

ArfGAP with coiled-coil, ankyrin repeat and PH domains 2, the group of ArfGAPs|BAR-PH domain containing|Ankyrin repeat domain containing

Basic information

Region (hg38): 3:195274744-195443044

Previous symbols: [ "CENTB2" ]

Links

ENSG00000114331 ∙ NCBI:23527 ∙ OMIM:607766 ∙ HGNC:16469 ∙ Uniprot:Q15057 ∙ 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 ACAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACAP2 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in ACAP2

This is a list of pathogenic ClinVar variants found in the ACAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-195279377-T-C		not specified	Uncertain significance (Aug 13, 2021)
3-195279401-C-T		not specified	Uncertain significance (Feb 11, 2022)
3-195291722-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-195291796-T-C		not specified	Uncertain significance (May 26, 2023)
3-195292431-G-A		not specified	Uncertain significance (Dec 13, 2021)
3-195292434-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-195292434-G-T		not specified	Uncertain significance (Aug 02, 2022)
3-195294748-G-A		not specified	Uncertain significance (Jan 20, 2023)
3-195297277-A-G		not specified	Uncertain significance (Mar 02, 2023)
3-195301971-A-C		not specified	Uncertain significance (Nov 18, 2022)
3-195306558-G-C		not specified	Uncertain significance (May 20, 2024)
3-195306602-T-G		not specified	Uncertain significance (Mar 15, 2024)
3-195320756-C-T		not specified	Uncertain significance (Nov 13, 2023)
3-195320772-A-C		not specified	Uncertain significance (Oct 06, 2021)
3-195326952-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-195333072-G-T		not specified	Uncertain significance (Apr 20, 2024)
3-195342478-A-C		not specified	Uncertain significance (May 01, 2023)
3-195342499-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-195381904-T-A		not specified	Uncertain significance (Jun 09, 2022)
3-195381908-C-T		not specified	Uncertain significance (Mar 18, 2024)
3-195381916-T-C		not specified	Uncertain significance (May 15, 2024)
3-195392120-A-G			Likely benign (Jun 13, 2018)
3-195442835-C-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACAP2	protein_coding	protein_coding	ENST00000326793	23	168343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.923	0.0767	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.22	224	407	0.551	0.0000208	5133
Missense in Polyphen		48	118.8	0.40404		1419
Synonymous	1.55	121	145	0.836	0.00000767	1373
Loss of Function	5.42	10	52.3	0.191	0.00000300	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6). {ECO:0000269|PubMed:11062263}.
• Pathway: Endocytosis - Homo sapiens (human);Arf6 signaling events (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.487
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.356
• hipred: Y
• hipred_score: 0.728
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acap2

Gene ontology

• Biological process: endocytic recycling;positive regulation of GTPase activity;cellular response to nerve growth factor stimulus
• Cellular component: endosome membrane;membrane
• Molecular function: GTPase activator activity;Rab GTPase binding;metal ion binding;phosphatidylinositol-3,5-bisphosphate binding