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

ENSG00000047365NCBI:116984OMIM:606645HGNC:16924Uniprot:Q8WZ64AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
2
missense
93
clinvar
4
clinvar
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)3128251
4-36068045-C-A not specified Uncertain significance (Jan 23, 2023)2477957
4-36068152-G-C not specified Uncertain significance (Jan 23, 2024)3128250
4-36068188-C-A not specified Uncertain significance (Jan 23, 2023)2478028
4-36068221-C-T not specified Uncertain significance (Apr 19, 2023)2538930
4-36068250-C-T not specified Uncertain significance (May 26, 2024)3309556
4-36080239-T-C not specified Uncertain significance (Jul 17, 2023)2612304
4-36080247-G-A not specified Likely benign (Jan 04, 2022)3128247
4-36082257-T-C not specified Uncertain significance (Dec 01, 2022)2331053
4-36082273-C-T not specified Uncertain significance (Dec 20, 2021)2346642
4-36083378-G-A not specified Uncertain significance (Jan 08, 2024)3128246
4-36083401-C-T not specified Uncertain significance (May 26, 2022)2291913
4-36091884-C-T Likely benign (Feb 01, 2023)2654706
4-36091909-C-T not specified Uncertain significance (May 06, 2022)2400664
4-36091930-C-T not specified Uncertain significance (Sep 06, 2022)2391369
4-36091931-G-A not specified Uncertain significance (Nov 09, 2021)2213394
4-36107583-T-C not specified Uncertain significance (Aug 13, 2021)2244744
4-36107589-C-T not specified Uncertain significance (Apr 01, 2024)3309545
4-36107607-C-T not specified Uncertain significance (Jan 20, 2023)2459746
4-36107613-G-C not specified Uncertain significance (Nov 17, 2023)3128245
4-36107649-G-A not specified Uncertain significance (Mar 30, 2024)3309566
4-36107675-T-C not specified Uncertain significance (Mar 15, 2024)3309639
4-36114203-C-G not specified Uncertain significance (Mar 01, 2024)3128244
4-36114223-G-T not specified Uncertain significance (May 26, 2023)2552146
4-36114251-C-T not specified Uncertain significance (Nov 07, 2022)2353837

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ARAP2protein_codingprotein_codingENST00000303965 32296289
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.77e-141.0012563811091257480.000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.8209238561.080.000043011223
Missense in Polyphen183204.860.893282817
Synonymous-0.4773163051.030.00001563112
Loss of Function4.993888.70.4280.000004751138

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008030.000799
Ashkenazi Jewish0.000.00
East Asian0.0002290.000217
Finnish0.0002850.000277
European (Non-Finnish)0.0005980.000571
Middle Eastern0.0002290.000217
South Asian0.0003700.000359
Other0.0003430.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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