ADAP1

ArfGAP with dual PH domains 1, the group of ArfGAPs|Pleckstrin homology domain containing

Basic information

Region (hg38): 7:897900-955407

Previous symbols: [ "CENTA1" ]

Links

ENSG00000105963 ∙ NCBI:11033 ∙ OMIM:608114 ∙ HGNC:16486 ∙ Uniprot:O75689 ∙ 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 ADAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAP1 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	2
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	18	1	1

Variants in ADAP1

This is a list of pathogenic ClinVar variants found in the ADAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-899138-C-T		not specified	Uncertain significance (Jun 09, 2022)
7-899208-C-T			Benign (Jun 18, 2018)
7-899233-A-G		not specified	Uncertain significance (Apr 28, 2023)
7-900538-C-T		not specified	Uncertain significance (Jul 12, 2022)
7-904137-C-G		not specified	Uncertain significance (May 29, 2024)
7-904206-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-904251-T-C		not specified	Uncertain significance (Feb 28, 2023)
7-905070-T-C		not specified	Uncertain significance (May 16, 2022)
7-905115-C-T		not specified	Uncertain significance (Aug 10, 2023)
7-905146-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-905146-G-C		not specified	Uncertain significance (Apr 22, 2024)
7-905167-G-A		not specified	Uncertain significance (May 31, 2023)
7-905180-G-C			Benign (Jun 18, 2018)
7-919976-T-G		not specified	Uncertain significance (Dec 16, 2023)
7-919979-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-920050-C-G		not specified	Uncertain significance (May 30, 2023)
7-926574-C-T		not specified	Uncertain significance (Sep 25, 2023)
7-926616-G-A		not specified	Uncertain significance (Jan 04, 2022)
7-926623-C-T		not specified	Uncertain significance (Jan 25, 2023)
7-926624-G-A			Likely benign (Dec 01, 2022)
7-935380-C-T		not specified	Uncertain significance (Nov 21, 2023)
7-935476-C-T		not specified	Uncertain significance (Dec 13, 2023)
7-954401-G-A		not specified	Uncertain significance (May 03, 2023)
7-954440-A-T		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAP1	protein_coding	protein_coding	ENST00000265846	11	57504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.533	0.467	125457	0	13	125470	0.0000518

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.888	188	226	0.834	0.0000152	2419
Missense in Polyphen		45	84.191	0.5345		835
Synonymous	-4.92	153	92.7	1.65	0.00000694	687
Loss of Function	3.59	5	24.0	0.209	0.00000144	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000104	0.0000924
European (Non-Finnish)	0.0000631	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for the ADP ribosylation factor family (Probable). Binds phosphatidylinositol 3,4,5- trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4). {ECO:0000269|PubMed:10448098, ECO:0000303|PubMed:10333475, ECO:0000305}.
• Pathway: Class I PI3K signaling events;Arf6 signaling events (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.390
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.775
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.653

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adap1

Gene ontology

• Biological process: cell surface receptor signaling pathway;regulation of GTPase activity;positive regulation of GTPase activity
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane
• Molecular function: GTPase activator activity;protein binding;phosphatidylinositol-3,4,5-trisphosphate binding;inositol 1,3,4,5 tetrakisphosphate binding;metal ion binding;phosphatidylinositol bisphosphate binding