GeneBe

ASAP1

protein-coding

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

Gene summary

This gene encodes an ADP-ribosylation factor (ARF) GTPase-activating protein. The GTPase-activating activity is stimulated by phosphatidylinositol 4,5-biphosphate (PIP2), and is greater towards ARF1 and ARF5, and lesser for ARF6. This gene maybe involved in regulation of membrane trafficking and cytoskeleton remodeling. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

Previous symbols:
  • DDEF1

MANE transcript

NM_018482.4

Inheritance

—

ClinVar variants

U:98B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr8:130,052,104-130,443,674

External References & Databases

Ensembl (ENSG00000153317)NCBI Gene (50807)OMIM (605953)HGNC:2720GenCCUniProt (Q9ULH1)AlphaFoldClinVar (ASAP1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~391.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ASAP1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 83
not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018482.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
2
clinvar
1
clinvar
 7
missense
85
clinvar
2
clinvar
 87
nonsense
1
clinvar
 1
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
6
clinvar
 6
Total009841103
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_018482.4RefSeqNP_060952.229MANE Select
ENST00000518721.6EnsemblENSP00000429900.129MANE Select
NM_001247996.2RefSeqNP_001234925.129Standard
NM_001362924.1RefSeqNP_001349853.130Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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

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

Molecular Function

  • phosphatidylserine binding
  • GTPase activator activity
  • protein binding
  • phosphatidylinositol-4,5-bisphosphate binding
  • phosphatidylinositol-3,4,5-trisphosphate binding

Cellular Component

  • podosome
  • cytosol
  • cell projection membrane
  • dendritic spine

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000357668
Coding exons
29
Length
391554
Individuals with no LoFs
125737
Homozygous LoFs
0
Heterozygous LoFs
10
Defined
125747
p
0.0000398
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.313756030.6210.00003137349
Missense (PolyPhen)126249.280.505453123
Synonymous-0.4772502411.040.00001352182
Loss of Function6.66663.10.09500.00000318770

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American00.0absent
Ashkenazi Jewish0.000100.000099rare
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000440.000044rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.177

Intolerance Scores

LoFtool
0.190
RVIS EVS
-1.24
RVIS percentile EVS
5.46

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Indispensability pred.
E
Indispensability score
0.850

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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