AGAP3 ArfGAP with GTPase domain, ankyrin repeat and PH domain 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AGAP3provided by HGNC
Official Full Name: ArfGAP with GTPase domain, ankyrin repeat and PH domain 3provided by HGNC
Primary source: HGNC:HGNC:16923
See related: Ensembl:ENSG00000133612 MIM:616813; AllianceGenome:HGNC:16923
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: CRAG; AGAP-3; CENTG3; MRIP-1; cnt-g3
Summary: This gene encodes an essential component of the N-methyl-D-aspartate (NMDA) receptor signaling complex which mediates long-term potentiation in synapses by linking activation of NMDA receptor to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor trafficking. The encoded protein contains an N-terminal GTPase-like domain, a pleckstrin homology domain, an ArfGAP domain and several C-terminal ankryn repeat domains. [provided by RefSeq, Apr 2017]
Expression: Ubiquitous expression in brain (RPKM 17.1), lung (RPKM 9.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q36.1

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (151085867..151144434)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (152258976..152317511)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (150782954..150841521)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

HUNK inhibits cargo uptake and lysosomal traffic in the caveolar pathway via the AGAP3/ARF6.
Title: HUNK inhibits cargo uptake and lysosomal traffic in the caveolar pathway via the AGAP3/ARF6.
Gastrointestinal stromal tumors with BRAF gene fusions. A report of two cases showing low or absent KIT expression resulting in diagnostic pitfalls.
Title: Gastrointestinal stromal tumors with BRAF gene fusions. A report of two cases showing low or absent KIT expression resulting in diagnostic pitfalls.
AGAP3 expression was significantly increased in colorectal cancer (CRC)and colorectal adenoma compared to normal tissue. CRAG overexpression up-regulated c-Jun expression, and significantly increased cell proliferation and colony formation capability. AGAP3 expression did not have a concordant association with patient prognosis among datasets
Title: CRMP5-associated GTPase (CRAG) Is a Candidate Driver Gene for Colorectal Cancer Carcinogenesis.
AGAP3 is an essential signaling component of the NMDA receptor complex that links NMDA receptor activation to AMPA receptor trafficking.
Title: AGAP3 and Arf6 regulate trafficking of AMPA receptors and synaptic plasticity.
M-RIP can assemble a complex containing both RhoA and Myosin phosphatase myosin binding subunit, suggesting that M-RIP may play a role in myosin phosphatase regulation by RhoA
Title: Myosin phosphatase-Rho interacting protein. A new member of the myosin phosphatase complex that directly binds RhoA.

Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH66056 (e-PCR)
- UniSTS:19469

GDB:4585228 (e-PCR)
- UniSTS:77716

MARC_12833-12834:1000491720:1 (e-PCR)
- UniSTS:267459

AF021133 (e-PCR)
- UniSTS:43985

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 GTPase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to reactive oxygen species	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell periphery	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density	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 3

Names: CRAM-associated GTPase; CRMP (collapsin response mediator protein) associated; MR1-interacting protein; centaurin-gamma-3

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_053086.1 RefSeqGene

Range

5645..63604

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001042535.4 → NP_001036000.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks several exons in the 3' coding region and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (b) has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AB209781, AC010973, BC044644

Consensus CDS

CCDS55185.1

UniProtKB/Swiss-Prot

Q96P47

UniProtKB/TrEMBL

Q86ST5

Related

ENSP00000418921.1, ENST00000473312.5

Conserved Domains (2) summary

cd04103
Location:128 → 285

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

smart00010
Location:126 → 291

small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily
NM_001281300.2 → NP_001268229.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform c

See identical proteins and their annotated locations for NP_001268229.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks two alternate exons in the 3' coding region, and initiates translation from a downstream start codon, compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC010973, AK055393

Consensus CDS

CCDS64802.1

UniProtKB/Swiss-Prot

Q96P47

UniProtKB/TrEMBL

Q86XV5

Related

ENSP00000418016.1, ENST00000463381.5

Conserved Domains (5) summary

cd00204
Location:458 → 547

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:173 → 314

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

sd00045
Location:458 → 488

ANK; ANK repeat [structural motif]

pfam01412
Location:333 → 447

ArfGap; Putative GTPase activating protein for Arf

cl21455
Location:1 → 57

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_001308304.2 → NP_001295233.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks several exons in the 3' coding region and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (d) has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AC010973, BC044644, BC069236

Consensus CDS

CCDS83243.1

UniProtKB/TrEMBL

C9J975

Related

ENSP00000418125.1, ENST00000479901.5

Conserved Domains (1) summary

cd04103
Location:128 → 285

Centaurin_gamma; Centaurin gamma (CENTG) GTPase
NM_001308305.2 → NP_001295234.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, has multiple coding region differences, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.

Source sequence(s)

AC010973, BC044644

Consensus CDS

CCDS78287.1

UniProtKB/TrEMBL

E7ESL9, Q86ST5

Related

ENSP00000335589.3, ENST00000335367.7

Conserved Domains (2) summary

cd04103
Location:308 → 465

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

smart00010
Location:306 → 471

small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily
NM_001350102.2 → NP_001337031.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks two alternate exons in the 3' coding region, compared to variant 1. The encoded isoform (f) is shorter than isoform a.

Source sequence(s)

AC010973

UniProtKB/Swiss-Prot

B3KNZ8, E9PAL8, Q59EN0, Q96P47, Q96RK3

UniProtKB/TrEMBL

A0A090N7Y0

Conserved Domains (5) summary

cd04103
Location:128 → 285

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

cd00204
Location:686 → 775

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:401 → 542

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

sd00045
Location:686 → 716

ANK; ANK repeat [structural motif]

pfam01412
Location:561 → 675

ArfGap; Putative GTPase activating protein for Arf
NM_001350103.2 → NP_001337032.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform g

Status: REVIEWED

Description

Transcript Variant: This variant (7) differs in the 5' UTR, contains an alternate internal exon, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (g) has a shorter and distinct N-terminus, compared to isoform a.

Source sequence(s)

AC010973

UniProtKB/TrEMBL

Q8N8Q2

Conserved Domains (5) summary

cd00204
Location:443 → 532

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:55 → 299

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

sd00045
Location:443 → 473

ANK; ANK repeat [structural motif]

pfam01412
Location:318 → 432

ArfGap; Putative GTPase activating protein for Arf

cl26386
Location:117 → 319

DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
NM_001350104.2 → NP_001337033.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform h

Status: REVIEWED

Description

Transcript Variant: This variant (8) differs in the 5' UTR, has multiple coding region differences, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (h) is shorter and has a distinct N-terminus, compared to isoform a.

Source sequence(s)

AC010973

Conserved Domains (4) summary

cd00204
Location:340 → 429

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:55 → 196

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

sd00045
Location:340 → 370

ANK; ANK repeat [structural motif]

pfam01412
Location:215 → 329

ArfGap; Putative GTPase activating protein for Arf
NM_031946.7 → NP_114152.3 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC010973, AF413079, BC048300

Consensus CDS

CCDS43681.1

UniProtKB/Swiss-Prot

B3KNZ8, E9PAL8, Q59EN0, Q96P47, Q96RK3

UniProtKB/TrEMBL

A0A090N7Y0

Related

ENSP00000380413.2, ENST00000397238.7

Conserved Domains (8) summary

cd04103
Location:128 → 285

Centaurin_gamma; Centaurin gamma (CENTG) GTPase

smart00010
Location:126 → 291

small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily

cd00204
Location:789 → 878

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:401 → 645

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

pfam00169
Location:404 → 465

PH; PH domain

pfam01412
Location:664 → 778

ArfGap; Putative GTPase activating protein for Arf

pfam12796
Location:789 → 879

Ank_2; Ankyrin repeats (3 copies)

sd00045
Location:789 → 819

ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

151085867..151144434

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419870.1 → XP_047275826.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X4
XM_047419866.1 → XP_047275822.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X1
XM_047419867.1 → XP_047275823.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X2
XM_047419868.1 → XP_047275824.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X3
XM_047419872.1 → XP_047275828.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X7
XM_047419871.1 → XP_047275827.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X6
XM_047419877.1 → XP_047275833.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X12
XM_047419873.1 → XP_047275829.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X8
XM_047419874.1 → XP_047275830.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X9
XM_047419878.1 → XP_047275834.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X13
XM_047419875.1 → XP_047275831.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X10
XM_047419876.1 → XP_047275832.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X11
XM_047419869.1 → XP_047275825.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X5
XM_011515780.3 → XP_011514082.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X5

See identical proteins and their annotated locations for XP_011514082.1

Conserved Domains (6) summary

PHA03307
Location:239 → 378

PHA03307; transcriptional regulator ICP4; Provisional

cd01250
Location:173 → 417

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

sd00045
Location:561 → 591

ANK; ANK repeat [structural motif]

cd08855
Location:434 → 542

ArfGap_AGAP3; ArfGAP with GTPase domain, ANK repeat and PH domain 3

pfam12796
Location:561 → 651

Ank_2; Ankyrin repeats (3 copies)

cl38936
Location:1 → 57

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RNA

XR_007059984.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

152258976..152317511

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054357209.1 → XP_054213184.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X4
XM_054357206.1 → XP_054213181.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X1
XM_054357207.1 → XP_054213182.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X2
XM_054357208.1 → XP_054213183.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X3
XM_054357213.1 → XP_054213188.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X7
XM_054357212.1 → XP_054213187.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X6
XM_054357218.1 → XP_054213193.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X12
XM_054357214.1 → XP_054213189.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X8
XM_054357215.1 → XP_054213190.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X9
XM_054357219.1 → XP_054213194.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X13
XM_054357216.1 → XP_054213191.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X10
XM_054357217.1 → XP_054213192.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X11
XM_054357211.1 → XP_054213186.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X5
XM_054357210.1 → XP_054213185.1 arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X5