ASAP2

ArfGAP with SH3 domain, ankyrin repeat and PH domain 2, the group of Ankyrin repeat domain containing|BAR-PH domain containing|ArfGAPs

Basic information

Region (hg38): 2:9206764-9405683

Previous symbols: [ "DDEF2" ]

Links

ENSG00000151693 ∙ NCBI:8853 ∙ OMIM:603817 ∙ HGNC:2721 ∙ Uniprot:O43150 ∙ 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 ASAP2 gene.

• Inborn genetic diseases (41 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASAP2 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	3	4
missense			40	1	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	4

Variants in ASAP2

This is a list of pathogenic ClinVar variants found in the ASAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-9207196-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-9279325-C-T			Benign (May 08, 2018)
2-9297350-G-A		not specified	Uncertain significance (Sep 27, 2022)
2-9318545-A-G		not specified	Uncertain significance (Feb 09, 2023)
2-9335156-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-9356285-A-G		not specified	Uncertain significance (Mar 13, 2023)
2-9356310-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-9356320-C-T			Benign (May 08, 2018)
2-9358777-A-G		not specified	Uncertain significance (Dec 12, 2023)
2-9368464-A-G		not specified	Uncertain significance (Jan 10, 2023)
2-9368498-A-G		not specified	Uncertain significance (Oct 27, 2021)
2-9374758-T-G		not specified	Uncertain significance (Jul 20, 2021)
2-9374804-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-9374804-G-T		not specified	Uncertain significance (Feb 09, 2022)
2-9374816-C-T		not specified	Uncertain significance (May 01, 2022)
2-9374828-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-9374851-C-T			Likely benign (Aug 16, 2018)
2-9374856-C-T		not specified	Uncertain significance (Jan 10, 2023)
2-9374858-G-A		not specified	Uncertain significance (Oct 02, 2023)
2-9374865-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-9374873-A-G		not specified	Uncertain significance (May 03, 2023)
2-9374892-C-T		not specified	Uncertain significance (Jul 13, 2021)
2-9374909-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-9374910-A-G		not specified	Uncertain significance (Dec 26, 2023)
2-9374923-A-T		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASAP2	protein_coding	protein_coding	ENST00000281419	28	198919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000367	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	429	591	0.726	0.0000350	6595
Missense in Polyphen		112	223.58	0.50094		2616
Synonymous	0.437	239	248	0.965	0.0000173	1901
Loss of Function	6.32	7	59.7	0.117	0.00000320	677

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000559	0.0000544
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates the small GTPases ARF1, ARF5 and ARF6. Regulates the formation of post-Golgi vesicles and modulates constitutive secretion. Modulates phagocytosis mediated by Fc gamma receptor and ARF6. Modulates PXN recruitment to focal contacts and cell migration. {ECO:0000269|PubMed:10022920, ECO:0000269|PubMed:10749932, ECO:0000269|PubMed:11304556}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Vitamin D Receptor Pathway;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;adp-ribosylation factor;Arf6 trafficking events (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.355
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.31

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.825
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.784

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asap2

Gene ontology

• Biological process: positive regulation of GTPase activity
• Cellular component: plasma membrane;Golgi cisterna membrane
• Molecular function: GTPase activator activity;protein binding;metal ion binding