AGAP1 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AGAP1provided by HGNC
Official Full Name: ArfGAP with GTPase domain, ankyrin repeat and PH domain 1provided by HGNC
Primary source: HGNC:HGNC:16922
See related: Ensembl:ENSG00000157985 MIM:608651; AllianceGenome:HGNC:16922
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GGAP1; AGAP-1; CENTG2; cnt-g2
Summary: This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression: Broad expression in brain (RPKM 11.1), colon (RPKM 5.1) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.2

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (235494043..236131793)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (235983538..236621510)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (236402687..237040437)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Crystal structure of the GTP-binding protein-like domain of AGAP1.
Title: Crystal structure of the GTP-binding protein-like domain of AGAP1.
CircAGAP1 promotes tumor progression by sponging miR-15-5p in clear cell renal cell carcinoma.
Title: CircAGAP1 promotes tumor progression by sponging miR-15-5p in clear cell renal cell carcinoma.
AGAP1 regulates subcellular localization of FilGAP and control cancer cell invasion.
Title: AGAP1 regulates subcellular localization of FilGAP and control cancer cell invasion.
2 Arf GAPs, ASAP1 and AGAP1, have been found to bind directly to and influence the activity of myosins and kinesins, motor proteins associated with filamentous actin and microtubules, respectively.
Title: Arf GAPs and molecular motors.
The effect of AGAP1 Knockdown could be rescued by FLAG-AGAP1, but not by an AGAP1 mutant that did not bind Kif2A efficiently, ArfGAP1-HA or Kif2A-GFP. The results support the hypothesis that the Kif2A.AGAP1 complex contributes to control of cytoskeleton remodeling involved in cell movement.
Title: Direct Functional Interaction of the Kinesin-13 Family Member Kinesin-like Protein 2A (Kif2A) and Arf GAP with GTP-binding Protein-like, Ankyrin Repeats and PH Domains1 (AGAP1).
GTP-binding protein-like domain of AGAP1 is protein binding site that allosterically regulates ArfGAP protein catalytic activity.
Title: GTP-binding protein-like domain of AGAP1 is protein binding site that allosterically regulates ArfGAP protein catalytic activity.
Observational study of gene-disease association. (HuGE Navigator)
Title: Evaluation of the chromosome 2q37.3 gene CENTG2 as an autism susceptibility gene.
AGAP1 is unique among the AZAPs in its specificity for Arf1, and this activity is dependent on its NH(2)-terminal GTPase-like domain. AGAP1 induce reciprocal activation of Arf6.
Title: Substrate specificities and activities of AZAP family Arf GAPs in vivo.
The AGAP1 has been found to associate with the adaptor protein complex AP-3 and regulate the function of AP-3 endosomes.
Title: The Arf GAPs AGAP1 and AGAP2 distinguish between the adaptor protein complexes AP-1 and AP-3.
overexpression inhibited formation of platelet-derived growth factor-induced ruffles and also induced loss of actin stress fibers
Title: AGAP1, an endosome-associated, phosphoinositide-dependent ADP-ribosylation factor GTPase-activating protein that affects actin cytoskeleton.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome wide association study of age at menarche in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies five new schizophrenia loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Genome-wide shRNA screening identifies AGAP1, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2S2202 (e-PCR), detects polymorphism
- UniSTS:35094

G63736 (e-PCR)
- UniSTS:140318

RH91277 (e-PCR)
- UniSTS:91935

SHGC-146098 (e-PCR)
- UniSTS:183343

FB3D10 (e-PCR)
- UniSTS:77120

D2S1397 (e-PCR), detects polymorphism
- UniSTS:65088

SHGC-154430 (e-PCR)
- UniSTS:183381

G32783 (e-PCR)
- UniSTS:117363

RH119441 (e-PCR)
- UniSTS:132982

RH122231 (e-PCR)
- UniSTS:134779

SHGC-146059 (e-PCR)
- UniSTS:174971

RH12556 (e-PCR)
- UniSTS:87165

STS-T94735 (e-PCR)
- UniSTS:25726

RH48088 (e-PCR)
- UniSTS:79235

SHGC-149056 (e-PCR)
- UniSTS:176772

SHGC-155949 (e-PCR)
- UniSTS:183429

SHGC-31743 (e-PCR)
- UniSTS:10395

RH102352 (e-PCR)
- UniSTS:96686

SHGC-80943 (e-PCR)
- UniSTS:102577

SHGC-146130 (e-PCR)
- UniSTS:175026

A009Q29 (e-PCR)
- UniSTS:40886

G33173 (e-PCR)
- UniSTS:51384

RH44862 (e-PCR)
- UniSTS:57797

SHGC-102168 (e-PCR)
- UniSTS:183241

WI-22093 (e-PCR)
- UniSTS:73418

D2S1421 (e-PCR)
- UniSTS:78569

G59791 (e-PCR)
- UniSTS:136942

SHGC-144496 (e-PCR)
- UniSTS:172273

G54615 (e-PCR)
- UniSTS:117748

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in activation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1

Names: Arf GAP with GTP-binding protein-like, ANK repeat and PH domains 1; GTP-binding and GTPase-activating protein 1; centaurin, gamma 2

NP_001032208.1

EC 3.6.5.2

NP_001231817.1

EC 3.6.5.2

NP_001399051.1

EC 3.6.5.2

NP_055729.2

EC 3.6.5.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_030314.1 RefSeqGene

Range

4955..642705

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001037131.3 → NP_001032208.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_001032208.1

Status: REVIEWED

Source sequence(s)

AC012305, AC019047, AK001722, AY033765, BC060814, BC140856, BC167153, CA446024

Consensus CDS

CCDS33408.1

UniProtKB/Swiss-Prot

B2RTX7, Q541S5, Q6P9D7, Q9NV93, Q9UPQ3

UniProtKB/TrEMBL

H7C211

Related

ENSP00000307634.7, ENST00000304032.13

Conserved Domains (8) summary

cd04103
Location:72 → 229

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

smart00173
Location:73 → 235

RAS; Ras subfamily of RAS small GTPases

cd00204
Location:736 → 825

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01250
Location:344 → 592

PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain

pfam00169
Location:347 → 411

PH; PH domain

pfam01412
Location:611 → 725

ArfGap; Putative GTPase activating protein for Arf

pfam12796
Location:736 → 826

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:768 → 799

ANK; ANK repeat [structural motif]
NM_001244888.2 → NP_001231817.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the allele encoded by the GRCh38 reference genome and encodes isoform 3.

Source sequence(s)

AC012305, AC064874, BC060814, BC167157

Consensus CDS

CCDS58756.1

UniProtKB/Swiss-Prot

Q9UPQ3

UniProtKB/TrEMBL

B2RZG9

Related

ENSP00000387174.1, ENST00000409457.5

Conserved Domains (2) summary

cd04103
Location:72 → 229

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

smart00173
Location:73 → 235

RAS; Ras subfamily of RAS small GTPases
NM_001412122.1 → NP_001399051.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses the same exon combination as variant 3 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. It encodes isoform 4 which is shorter and has a distinct C-terminus, compared to isoform 3.

Source sequence(s)

CP068276
NM_014914.5 → NP_055729.2 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 2

Status: REVIEWED

Source sequence(s)

AC012305, AC019047, AF413078, AK001722, AY033765, BC060814, BC140856, CA446024

Consensus CDS

CCDS2514.1

UniProtKB/TrEMBL

B2RZG9

Related

ENSP00000338378.5, ENST00000336665.9

Conserved Domains (8) summary

cd04103
Location:72 → 229

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

smart00173
Location:73 → 235

RAS; Ras subfamily of RAS small GTPases

cd00204
Location:683 → 772

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

cd01250
Location:344 → 539

PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain

pfam00169
Location:347 → 411

PH; PH domain

pfam01412
Location:558 → 672

ArfGap; Putative GTPase activating protein for Arf

pfam12796
Location:683 → 773

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:715 → 746

ANK; ANK repeat [structural motif]