ARAP1

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1, the group of Sterile alpha motif domain containing|ArfGAPs|Ankyrin repeat domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 11:72685069-72793599

Previous symbols: [ "CENTD2" ]

Links

ENSG00000186635 ∙ NCBI:116985 ∙ OMIM:606646 ∙ HGNC:16925 ∙ Uniprot:Q96P48 ∙ 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 ARAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARAP1 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	2	3
missense			98	5	3	106
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1	1	5
Total	0	0	101	7	6

Variants in ARAP1

This is a list of pathogenic ClinVar variants found in the ARAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-72685669-C-T		not specified	Uncertain significance (Feb 09, 2023)
11-72686055-G-A		not specified	Uncertain significance (Mar 03, 2022)
11-72686100-C-T		not specified	Uncertain significance (Nov 18, 2022)
11-72686107-G-C		not specified	Uncertain significance (Jul 11, 2023)
11-72686148-C-A		not specified	Uncertain significance (Apr 05, 2023)
11-72686149-G-A		not specified	Uncertain significance (Nov 03, 2023)
11-72686155-C-T			Benign (Jun 20, 2018)
11-72686158-G-A		not specified	Uncertain significance (Dec 13, 2021)
11-72687451-A-T		not specified	Uncertain significance (Jun 21, 2021)
11-72687471-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-72692775-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-72693326-C-T		not specified	Uncertain significance (Oct 26, 2021)
11-72693327-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-72693395-G-A		not specified	Uncertain significance (Apr 12, 2023)
11-72693396-G-C		not specified	Uncertain significance (Apr 12, 2023)
11-72693446-T-C		not specified	Uncertain significance (Jul 27, 2021)
11-72693464-C-T		not specified	Likely benign (Aug 22, 2023)
11-72693802-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-72695046-G-A		not specified	Uncertain significance (Apr 05, 2023)
11-72695392-T-A		not specified	Uncertain significance (Sep 07, 2022)
11-72695395-G-A		not specified	Uncertain significance (Dec 05, 2022)
11-72695430-A-G		not specified	Uncertain significance (Feb 22, 2023)
11-72695449-C-T		not specified	Uncertain significance (Nov 27, 2023)
11-72695559-T-C		not specified	Uncertain significance (Apr 19, 2024)
11-72695761-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARAP1	protein_coding	protein_coding	ENST00000393609	33	108531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.123	0.877	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	729	910	0.801	0.0000623	9228
Missense in Polyphen		224	328.42	0.68206		3351
Synonymous	0.977	350	374	0.936	0.0000252	2987
Loss of Function	6.14	18	75.7	0.238	0.00000389	833

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000275
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000221	0.000217
Finnish	0.000326	0.000323
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000221	0.000217
South Asian	0.000202	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating protein that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members. Is activated by phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) binding. Can be activated by phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding, albeit with lower efficiency. Has a preference for ARF1 and ARF5 (By similarity). {ECO:0000250, ECO:0000269|PubMed:11804590}.
• Pathway: Endocytosis - Homo sapiens (human);Signaling by PTK6;Signal Transduction;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1;Rho GTPase cycle;adp-ribosylation factor;Signaling by Rho GTPases;EGFR1;Signaling by Non-Receptor Tyrosine Kinases;PDGFR-beta signaling pathway;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.775
• rvis_EVS: -1.45
• rvis_percentile_EVS: 3.93

Haploinsufficiency Scores

• pHI: 0.246
• hipred: Y
• hipred_score: 0.637
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arap1
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: positive regulation of receptor recycling;signal transduction;regulation of cell shape;actin filament reorganization involved in cell cycle;positive regulation of GTPase activity;positive regulation of epidermal growth factor receptor signaling pathway;regulation of small GTPase mediated signal transduction;regulation of cellular component movement;positive regulation of filopodium assembly;negative regulation of stress fiber assembly
• Cellular component: nucleoplasm;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;cytoplasmic vesicle;Golgi cisterna membrane;intracellular membrane-bounded organelle
• Molecular function: GTPase activator activity;protein binding;phosphatidylinositol-3,4,5-trisphosphate binding;type 1 angiotensin receptor binding;metal ion binding