ASAP3

ArfGAP with SH3 domain, ankyrin repeat and PH domain 3, the group of Ankyrin repeat domain containing|ArfGAPs|BAR-PH domain containing

Basic information

Region (hg38): 1:23428563-23484637

Previous symbols: [ "DDEFL1" ]

Links

ENSG00000088280 ∙ NCBI:55616 ∙ OMIM:616594 ∙ HGNC:14987 ∙ Uniprot:Q8TDY4 ∙ 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 ASAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASAP3 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			44	3	1	48
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	44	5	2

Variants in ASAP3

This is a list of pathogenic ClinVar variants found in the ASAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23431036-G-T			Likely benign (Jun 11, 2018)
1-23431091-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-23431093-G-A		not specified	Uncertain significance (Jun 02, 2023)
1-23431099-C-T		not specified	Uncertain significance (Jun 19, 2024)
1-23431103-G-A		not specified	Uncertain significance (Jan 18, 2022)
1-23431121-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-23431706-C-A		not specified	Uncertain significance (Oct 27, 2022)
1-23431706-C-T		not specified	Uncertain significance (Aug 17, 2021)
1-23431757-A-T		not specified	Uncertain significance (Jan 09, 2024)
1-23431799-G-A		not specified	Uncertain significance (Mar 27, 2023)
1-23431916-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-23433116-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-23433119-A-G		not specified	Uncertain significance (Mar 21, 2024)
1-23433175-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-23433176-C-A		not specified	Uncertain significance (Jan 04, 2022)
1-23433250-G-T			Likely benign (May 01, 2023)
1-23433251-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-23433252-C-T			Likely benign (Sep 01, 2022)
1-23433272-G-T		not specified	Uncertain significance (Dec 28, 2022)
1-23433475-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-23433516-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-23433643-T-C		not specified	Uncertain significance (Dec 01, 2022)
1-23434295-C-G		not specified	Uncertain significance (Jan 12, 2024)
1-23434320-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-23435873-G-A		not specified	Likely benign (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASAP3	protein_coding	protein_coding	ENST00000336689	25	56006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.33e-12	1.00	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	435	522	0.833	0.0000313	5841
Missense in Polyphen		132	181.36	0.72785		2043
Synonymous	1.65	191	222	0.859	0.0000146	1776
Loss of Function	3.25	27	52.4	0.515	0.00000281	578

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000526	0.000526
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000168	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000168	0.000163
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell proliferation. {ECO:0000269|PubMed:14654939}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.944
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.25

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.747
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.360

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asap3

Gene ontology

• Biological process: cell migration;positive regulation of GTPase activity;regulation of stress fiber assembly
• Cellular component: ruffle;nucleoplasm;cytosol;focal adhesion;intracellular membrane-bounded organelle
• Molecular function: GTPase activator activity;protein binding;metal ion binding