ASAP1

ArfGAP with SH3 domain, ankyrin repeat and PH domain 1, the group of BAR-PH domain containing|ArfGAPs|Ankyrin repeat domain containing

Basic information

Region (hg38): 8:130052103-130443674

Previous symbols: [ "DDEF1" ]

Links

ENSG00000153317 ∙ NCBI:50807 ∙ OMIM:605953 ∙ HGNC:2720 ∙ Uniprot:Q9ULH1 ∙ 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 ASAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASAP1 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	1	3
missense			26	1		27
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	26	3	1

Variants in ASAP1

This is a list of pathogenic ClinVar variants found in the ASAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-130054750-A-G		not specified	Uncertain significance (Nov 17, 2023)
8-130054796-T-C		not specified	Uncertain significance (Jul 12, 2023)
8-130060580-G-A		not specified	Uncertain significance (Jun 07, 2023)
8-130060609-C-T			Likely benign (Mar 01, 2023)
8-130060635-C-T		not specified	Uncertain significance (Sep 16, 2021)
8-130060667-G-C		not specified	Uncertain significance (Sep 29, 2022)
8-130060703-G-A		not specified	Uncertain significance (Dec 09, 2023)
8-130060904-G-A		not specified	Uncertain significance (Nov 14, 2023)
8-130060957-G-A			Likely benign (Mar 01, 2023)
8-130079925-A-C		not specified	Uncertain significance (Jan 06, 2023)
8-130092048-C-T		not specified	Uncertain significance (Apr 01, 2024)
8-130092093-C-T		not specified	Uncertain significance (Apr 05, 2023)
8-130092114-G-T		not specified	Uncertain significance (Sep 12, 2023)
8-130092116-G-A		not specified	Uncertain significance (Jan 16, 2024)
8-130112132-G-A		not specified	Uncertain significance (Oct 26, 2021)
8-130112133-T-C		not specified	Likely benign (Sep 27, 2022)
8-130112246-T-C		not specified	Uncertain significance (May 31, 2023)
8-130112258-G-A		not specified	Uncertain significance (Jul 19, 2023)
8-130116694-G-C		not specified	Uncertain significance (Oct 27, 2022)
8-130118183-C-T		not specified	Uncertain significance (Apr 07, 2022)
8-130118216-C-T		not specified	Uncertain significance (Jun 22, 2021)
8-130118535-T-C		not specified	Uncertain significance (Feb 07, 2023)
8-130118542-G-T		not specified	Uncertain significance (May 08, 2023)
8-130118634-T-C		not specified	Uncertain significance (Jul 30, 2023)
8-130128010-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASAP1	protein_coding	protein_coding	ENST00000357668	29	391554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000197	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.31	375	603	0.621	0.0000313	7349
Missense in Polyphen		126	249.28	0.50545		3123
Synonymous	-0.477	250	241	1.04	0.0000135	2182
Loss of Function	6.66	6	63.1	0.0950	0.00000318	770

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses phosphatidylinositol 4,5-bisphosphate- dependent GTPase-activating protein activity for ARF1 (ADP ribosylation factor 1) and ARF5 and a lesser activity towards ARF6. May coordinate membrane trafficking with cell growth or actin cytoskeleton remodeling by binding to both SRC and PIP2. May function as a signal transduction protein involved in the differentiation of fibroblasts into adipocytes and possibly other cell types (By similarity). Plays a role in ciliogenesis. {ECO:0000250, ECO:0000269|PubMed:20393563}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);EGF-EGFR Signaling Pathway;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;adp-ribosylation factor;EGFR1;Arf1 pathway;VxPx cargo-targeting to cilium;Signaling events mediated by focal adhesion kinase;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.190
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.745
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asap1

Gene ontology

• Biological process: positive regulation of GTPase activity;cilium assembly;negative regulation of dendritic spine development;positive regulation of podosome assembly;positive regulation of membrane tubulation
• Cellular component: podosome;cytosol;cell projection membrane;dendritic spine
• Molecular function: phosphatidylserine binding;GTPase activator activity;protein binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;cadherin binding;metal ion binding