ARAP1 ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ARAP1provided by HGNC
Official Full Name: ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1provided by HGNC
Primary source: HGNC:HGNC:16925
See related: Ensembl:ENSG00000186635 MIM:606646; AllianceGenome:HGNC:16925
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: CENTD2; cnt-d2
Summary: The protein encoded by this gene contains SAM, ARF-GAP, RHO-GAP, ankyrin repeat, RAS-associating, and pleckstrin homology (PH) domains. In vitro, this protein displays RHO-GAP and phosphatidylinositol (3,4,5) trisphosphate (PIP3)-dependent ARF-GAP activity. The encoded protein associates with the Golgi, and the ARF-GAP activity mediates changes in the Golgi and the formation of filopodia. It is thought to regulate the cell-specific trafficking of a receptor protein involved in apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
Expression: Ubiquitous expression in spleen (RPKM 32.0), appendix (RPKM 25.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.4

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (72685069..72752408, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (72613306..72680645, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (72396114..72463453, complement)

Chromosome 11 - NC_000011.10 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?

Arap1 loss causes retinal pigment epithelium phagocytic dysfunction and subsequent photoreceptor death.
Title: Arap1 loss causes retinal pigment epithelium phagocytic dysfunction and subsequent photoreceptor death.
Deep Resequencing of 9 Candidate Genes Identifies a Role for ARAP1 and IGF2BP2 in Modulating Insulin Secretion Adjusted for Insulin Resistance in Obese Southern Europeans.
Title: Deep Resequencing of 9 Candidate Genes Identifies a Role for ARAP1 and IGF2BP2 in Modulating Insulin Secretion Adjusted for Insulin Resistance in Obese Southern Europeans.
Identifying the association between single nucleotide polymorphisms in KCNQ1, ARAP1, and KCNJ11 and type 2 diabetes mellitus in a Chinese population.
Title: Identifying the association between single nucleotide polymorphisms in KCNQ1, ARAP1, and KCNJ11 and type 2 diabetes mellitus in a Chinese population.
LncRNA ARAP1-AS2 promotes high glucose-induced human proximal tubular cell injury via persistent transactivation of the EGFR by interacting with ARAP1.
Title: LncRNA ARAP1-AS2 promotes high glucose-induced human proximal tubular cell injury via persistent transactivation of the EGFR by interacting with ARAP1.
Increased long non-coding RNA ARAP1-AS1 expression and its prognostic significance in human gastric cancer: a preliminary study.
Title: Increased long non-coding RNA ARAP1-AS1 expression and its prognostic significance in human gastric cancer: a preliminary study.
The effect of lncRNA-ARAP1-AS2/ARAP1 on high glucose-induced cytoskeleton rearrangement and epithelial-mesenchymal transition in human renal tubular epithelial cells.
Title: The effect of lncRNA-ARAP1-AS2/ARAP1 on high glucose-induced cytoskeleton rearrangement and epithelial-mesenchymal transition in human renal tubular epithelial cells.
Low expression of ARAP1 is an independent prognostic biomarker of shorter recurrence free survival in older patients with high grade ovarian serous carcinoma receiving first-line platinum-based antineoplastic therapy.
Title: ARAP1 is an independent prognostic biomarker in older women with ovarian high-grade serous adenocarcinoma receiving first-line platinum-based antineoplastic therapy.
Quantitative trait loci genes analysis reveals association between T2D risk variants at the ARAP1/STARD10 locus and STARD10 but not ARAP1 expression.
Title: Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice.
Genetic variant rs1552224 of CENTD2 on chromosome 11 contributes to an independent effect as well as joint cumulative effect with rs2237897 of KCNQ1 on the risk of type 2 diabetes mellitus in Chinese Han population.
Title: Joint effect of CENTD2 and KCNQ1 polymorphisms on the risk of type 2 diabetes mellitus among Chinese Han population.
The proinsulin-decreasing and T2D-risk Alleles are associated with increased ARAP1 mRNA levels in primary human pancreatic islets.
Title: A common functional regulatory variant at a type 2 diabetes locus upregulates ARAP1 expression in the pancreatic beta cell.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A006F43 (e-PCR)
- UniSTS:63496

D11S1002 (e-PCR)
- UniSTS:68645

SHGC-156281 (e-PCR)
- UniSTS:182474

SHGC-148738 (e-PCR)
- UniSTS:176587

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables GTPase activator activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-3,4,5-trisphosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3,4,5-trisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables type 1 angiotensin receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in actin filament organization	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of GTPase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of filopodium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of receptor recycling	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell shape	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell shape	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of small GTPase mediated signal transduction	TAS Traceable Author Statement more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi cisterna membrane	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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

Names: ARF-GAP, RHO-GAP, ankyrin repeat, and pleckstrin homology domains-containing protein 1; centaurin-delta-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.

mRNA and Protein(s)

NM_001040118.3 → NP_001035207.1 arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 isoform c

See identical proteins and their annotated locations for NP_001035207.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) is the longest transcript and it encodes the longest protein (isoform c).

Source sequence(s)

AP003065, AY553630, BC008315

Consensus CDS

CCDS41687.1

UniProtKB/Swiss-Prot

A3KLL7, B2RTS2, O94879, Q4LDD5, Q59FI7, Q6PHS3, Q8WU51, Q96HP6, Q96L71, Q96P48

UniProtKB/TrEMBL

A0A2X0SFK3

Related

ENSP00000377233.3, ENST00000393609.8

Conserved Domains (11) summary

cd09490
Location:6 → 68

SAM_Arap1,2,3; SAM domain of Arap1,2,3 (angiotensin receptor-associated protein)

smart00454
Location:10 → 64

SAM; Sterile alpha motif

cd04385
Location:956 → 1135

RhoGAP_ARAP; RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ...

cd13253
Location:329 → 421

PH1_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 1

cd13254
Location:436 → 525

PH2_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 2

cd13256
Location:743 → 849

PH3_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 3

cd13257
Location:862 → 952

PH4_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 4

cd13259
Location:1263 → 1402

PH5_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 5

pfam00169
Location:328 → 419

PH; PH domain

pfam00788
Location:1172 → 1261

RA; Ras association (RalGDS/AF-6) domain

pfam01412
Location:535 → 651

ArfGap; Putative GTPase activating protein for Arf
NM_001135190.2 → NP_001128662.1 arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 isoform d

See identical proteins and their annotated locations for NP_001128662.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and lacks two alternate in-frame coding exons, compared to variant 3. the resulting protein (isoform d) has a shorter N-terminus and lacks the SAM domain and portions of the ArfGAP and fifth PH domains, compared to isoform c.

Source sequence(s)

AP003065, BC008315, BC140792, DA186424

Consensus CDS

CCDS44671.1

UniProtKB/TrEMBL

B7ZMI2

Related

ENSP00000403127.1, ENST00000429686.5

Conserved Domains (9) summary

cd04385
Location:650 → 829

RhoGAP_ARAP; RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ...

cd13253
Location:84 → 176

PH1_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 1

cd13254
Location:191 → 280

PH2_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 2

cd13256
Location:437 → 543

PH3_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 3

cd13257
Location:556 → 646

PH4_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 4

cd13259
Location:957 → 1085

PH5_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 5

pfam00169
Location:83 → 174

PH; PH domain

pfam00788
Location:866 → 955

RA; Ras association (RalGDS/AF-6) domain

pfam01412
Location:290 → 362

ArfGap; Putative GTPase activating protein for Arf
NM_001369489.1 → NP_001356418.1 arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 isoform e

Status: REVIEWED

Source sequence(s)

AP003065

Consensus CDS

CCDS91531.1

UniProtKB/TrEMBL

B7ZMI2, E7EU13

Related

ENSP00000392264.1, ENST00000426523.5

Conserved Domains (8) summary

cd04385
Location:711 → 890

RhoGAP_ARAP; RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity ...

cd13253
Location:84 → 176

PH1_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 1

cd13254
Location:191 → 280

PH2_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 2

cd13256
Location:498 → 604

PH3_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 3

cd13257
Location:617 → 707

PH4_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 4

cd13259
Location:1018 → 1146

PH5_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 5

cd17226
Location:926 → 1018

RA_ARAP1; Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 (ARAP1)

cd08837
Location:290 → 405

ArfGap_ARAP; ArfGap with Rho-Gap domain, ANK repeat and PH domain-containing proteins
NM_015242.5 → NP_056057.2 arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 isoform a

See identical proteins and their annotated locations for NP_056057.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 5' UTR, compared to variant 3. This difference causes translation initiation at a downstream AUG and an isoform (a) with a shorter N-terminus compared to isoform c.

Source sequence(s)

AB018325, BC008315, DA186424

Consensus CDS

CCDS8217.2

UniProtKB/TrEMBL

A0A2X0SFK3

Related

ENSP00000335506.8, ENST00000334211.12

Conserved Domains (9) summary

cd04385
Location:711 → 890

RhoGAP_ARAP; RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ...

cd13253
Location:84 → 176

PH1_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 1

cd13254
Location:191 → 280

PH2_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 2

cd13256
Location:498 → 604

PH3_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 3

cd13257
Location:617 → 707

PH4_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 4

cd13259
Location:1018 → 1157

PH5_ARAP; ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 5

pfam00169
Location:83 → 174

PH; PH domain

pfam00788
Location:927 → 1016

RA; Ras association (RalGDS/AF-6) domain

pfam01412
Location:290 → 406

ArfGap; Putative GTPase activating protein for Arf