ADAP2

ArfGAP with dual PH domains 2, the group of Pleckstrin homology domain containing|ArfGAPs

Basic information

Region (hg38): 17:30906344-30959945

Previous symbols: [ "CENTA2" ]

Links

ENSG00000184060 ∙ NCBI:55803 ∙ OMIM:608635 ∙ HGNC:16487 ∙ Uniprot:Q9NPF8 ∙ 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 ADAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAP2 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in ADAP2

This is a list of pathogenic ClinVar variants found in the ADAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-30922054-C-G		not specified	Uncertain significance (Dec 15, 2023)
17-30922945-G-A		not specified	Uncertain significance (Apr 08, 2024)
17-30923056-G-C		not specified	Uncertain significance (Dec 12, 2023)
17-30923062-A-G		not specified	Uncertain significance (Aug 21, 2023)
17-30926830-A-T		not specified	Uncertain significance (Feb 26, 2024)
17-30926852-G-A		not specified	Uncertain significance (Dec 07, 2021)
17-30926859-G-T		not specified	Uncertain significance (Jan 30, 2024)
17-30926896-A-C		not specified	Uncertain significance (Feb 17, 2023)
17-30926917-C-G		not specified	Uncertain significance (Dec 16, 2023)
17-30931930-G-A		not specified	Likely benign (May 05, 2023)
17-30934221-A-G		not specified	Uncertain significance (Dec 15, 2022)
17-30934269-G-T		not specified	Uncertain significance (Feb 06, 2023)
17-30944914-G-T		not specified	Uncertain significance (Jul 19, 2022)
17-30945046-G-A		not specified	Uncertain significance (Apr 22, 2024)
17-30945047-T-A		not specified	Uncertain significance (Sep 28, 2022)
17-30949294-T-A		not specified	Uncertain significance (Apr 12, 2024)
17-30949315-G-A		not specified	Uncertain significance (Nov 17, 2022)
17-30953331-T-C		not specified	Uncertain significance (Apr 07, 2022)
17-30954508-G-A		not specified	Uncertain significance (Apr 18, 2023)
17-30956250-G-A		not specified	Uncertain significance (Dec 02, 2022)
17-30956257-G-T		not specified	Uncertain significance (May 20, 2024)
17-30956287-G-T		not specified	Uncertain significance (Oct 13, 2023)
17-30956322-C-G		not specified	Uncertain significance (May 29, 2024)
17-30956376-G-C		not specified	Uncertain significance (Mar 02, 2023)
17-30956463-C-T			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAP2	protein_coding	protein_coding	ENST00000330889	11	52979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.24e-10	0.563	125567	2	179	125748	0.000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.803	172	204	0.842	0.0000116	2496
Missense in Polyphen		66	88.782	0.74339		1131
Synonymous	0.832	66	75.2	0.878	0.00000397	715
Loss of Function	1.26	18	24.8	0.727	0.00000137	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000663	0.000662
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000973	0.000924
European (Non-Finnish)	0.00122	0.00120
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family (Potential). Binds phosphatidylinositol 3,4,5- trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). Possesses a stoichiometry of two binding sites for InsP4 with identical affinity. {ECO:0000269|PubMed:14690521, ECO:0000305}.
• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.739
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.0830
• hipred: N
• hipred_score: 0.296
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.512

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adap2

Zebrafish Information Network

• Gene name: adap2
• Affected structure: atrioventricular valve
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: heart development;positive regulation of GTPase activity
• Cellular component: cytoplasm;mitochondrial envelope;plasma membrane
• Molecular function: GTPase activator activity;protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;protein binding, bridging;phosphatidylinositol-3,4-bisphosphate binding;inositol 1,3,4,5 tetrakisphosphate binding;metal ion binding