ARAP2

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2, the group of Ankyrin repeat domain containing|Pleckstrin homology domain containing|Sterile alpha motif domain containing|ArfGAPs

Basic information

Region (hg38): 4:35948221-36244514

Previous symbols: [ "CENTD1" ]

Links

ENSG00000047365 ∙ NCBI:116984 ∙ OMIM:606645 ∙ HGNC:16924 ∙ Uniprot:Q8WZ64 ∙ 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 ARAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARAP2 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				2		2
missense			93	4		97
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	93	6	0

Variants in ARAP2

This is a list of pathogenic ClinVar variants found in the ARAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-36067919-C-A		not specified	Uncertain significance (Sep 17, 2021)
4-36068045-C-A		not specified	Uncertain significance (Jan 23, 2023)
4-36068152-G-C		not specified	Uncertain significance (Jan 23, 2024)
4-36068188-C-A		not specified	Uncertain significance (Jan 23, 2023)
4-36068221-C-T		not specified	Uncertain significance (Apr 19, 2023)
4-36068250-C-T		not specified	Uncertain significance (May 26, 2024)
4-36080239-T-C		not specified	Uncertain significance (Jul 17, 2023)
4-36080247-G-A		not specified	Likely benign (Jan 04, 2022)
4-36082257-T-C		not specified	Uncertain significance (Dec 01, 2022)
4-36082273-C-T		not specified	Uncertain significance (Dec 20, 2021)
4-36083378-G-A		not specified	Uncertain significance (Jan 08, 2024)
4-36083401-C-T		not specified	Uncertain significance (May 26, 2022)
4-36091884-C-T			Likely benign (Feb 01, 2023)
4-36091909-C-T		not specified	Uncertain significance (May 06, 2022)
4-36091930-C-T		not specified	Uncertain significance (Sep 06, 2022)
4-36091931-G-A		not specified	Uncertain significance (Nov 09, 2021)
4-36107583-T-C		not specified	Uncertain significance (Aug 13, 2021)
4-36107589-C-T		not specified	Uncertain significance (Apr 01, 2024)
4-36107607-C-T		not specified	Uncertain significance (Jan 20, 2023)
4-36107613-G-C		not specified	Uncertain significance (Nov 17, 2023)
4-36107649-G-A		not specified	Uncertain significance (Mar 30, 2024)
4-36107675-T-C		not specified	Uncertain significance (Mar 15, 2024)
4-36114203-C-G		not specified	Uncertain significance (Mar 01, 2024)
4-36114223-G-T		not specified	Uncertain significance (May 26, 2023)
4-36114251-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARAP2	protein_coding	protein_coding	ENST00000303965	32	296289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.77e-14	1.00	125638	1	109	125748	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.820	923	856	1.08	0.0000430	11223
Missense in Polyphen		183	204.86	0.89328		2817
Synonymous	-0.477	316	305	1.03	0.0000156	3112
Loss of Function	4.99	38	88.7	0.428	0.00000475	1138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000803	0.000799
Ashkenazi Jewish	0.00	0.00
East Asian	0.000229	0.000217
Finnish	0.000285	0.000277
European (Non-Finnish)	0.000598	0.000571
Middle Eastern	0.000229	0.000217
South Asian	0.000370	0.000359
Other	0.000343	0.000326

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 (By similarity). {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human);Signal Transduction;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;Rho GTPase cycle;adp-ribosylation factor;Signaling by Rho GTPases;Arf6 signaling events (Consensus)

Intolerance Scores

• loftool: 0.897
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.17

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.448
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arap2
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol
• Molecular function: GTPase activator activity;phosphatidylinositol-3,4,5-trisphosphate binding;metal ion binding