FARP1 FERM, ARH/RhoGEF and pleckstrin domain protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FARP1provided by HGNC
Official Full Name: FERM, ARH/RhoGEF and pleckstrin domain protein 1provided by HGNC
Primary source: HGNC:HGNC:3591
See related: Ensembl:ENSG00000152767 MIM:602654; AllianceGenome:HGNC:3591
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: CDEP; GLCC1; PLEKHC2; PPP1R75; FARP1-IT1
Summary: This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]
Expression: Ubiquitous expression in kidney (RPKM 19.9), thyroid (RPKM 13.0) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q32.2

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (98142589..98455176)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (97349662..97662977)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (98794843..99107430)

Chromosome 13 - NC_000013.11 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?

circFARP1 enables cancer-associated fibroblasts to promote gemcitabine resistance in pancreatic cancer via the LIF/STAT3 axis.
Title: circFARP1 enables cancer-associated fibroblasts to promote gemcitabine resistance in pancreatic cancer via the LIF/STAT3 axis.
FARP1, ARHGEF39, and TIAM2 are essential receptor tyrosine kinase effectors for Rac1-dependent cell motility in human lung adenocarcinoma.
Title: FARP1, ARHGEF39, and TIAM2 are essential receptor tyrosine kinase effectors for Rac1-dependent cell motility in human lung adenocarcinoma.
FARP1 facilitates malignant melanoma cell proliferation and migration by modulating the MAPK signaling pathway.
Title: FARP1 Facilitates Cell Proliferation Through Modulating MAPK Signaling Pathway in Cutaneous Melanoma.
We have reported here for the first time a reduced activity of both Rac1 and Cdc42 in human pheochromocytoma resection as well as tumor-associated expression changes of FARP1, ARHGEF1, and ARHGAP36
Title: Cdc42 and Rac1 activity is reduced in human pheochromocytoma and correlates with FARP1 and ARHGEF1 expression.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Meta-analysis of gene-disease association. (HuGE Navigator)
Title: Non-replication of association for six polymorphisms from meta-analysis of genome-wide association studies of Parkinson's disease: large-scale collaborative study.

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

EBI GWAS Catalog

Description
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies new susceptibility loci for migraine. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Voxelwise genome-wide association study (vGWAS). 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

RH102179 (e-PCR)
- UniSTS:96513

D13S159 (e-PCR), detects polymorphism
- UniSTS:15106

RH93030 (e-PCR)
- UniSTS:86019

RH79725 (e-PCR)
- UniSTS:86542

G09892 (e-PCR)
- UniSTS:22301

WI-10746 (e-PCR)
- UniSTS:65310

SHGC-149744 (e-PCR)
- UniSTS:177191

PMC156606P2 (e-PCR)
- UniSTS:271409

PMC156606P3 (e-PCR)
- UniSTS:271410

D8S2279 (e-PCR)
- UniSTS:473907

G54126 (e-PCR)
- UniSTS:109363

AFM210wb6 (e-PCR)
- UniSTS:70196

SHGC-111725 (e-PCR)
- UniSTS:168513

D13S1298 (e-PCR), detects polymorphism
- UniSTS:46402

D13S159 (e-PCR), detects polymorphism
- UniSTS:50499

STS-AA007218 (e-PCR)
- UniSTS:53318

D13S896 (e-PCR)
- UniSTS:337

G60059 (e-PCR)
- UniSTS:137321

D13S1192 (e-PCR)
- UniSTS:8049

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

D13S671E (e-PCR)
- UniSTS:153203

D13S674E (e-PCR)
- UniSTS:153207

D13S680E (e-PCR)
- UniSTS:153213

D11S3114 (e-PCR)
- UniSTS:152207

RH47601 (e-PCR)
- UniSTS:27288

D13S1378 (e-PCR)
- UniSTS:47268

HSC02G012 (e-PCR)
- UniSTS:11688

RH44997 (e-PCR)
- UniSTS:4783

SHGC-154508 (e-PCR)
- UniSTS:182710

A006I40 (e-PCR)
- UniSTS:56247

STS-H78565 (e-PCR)
- UniSTS:11960

WI-14178 (e-PCR)
- UniSTS:20413

D13S128 (e-PCR)
- UniSTS:147647

D13S128 (e-PCR)
- UniSTS:147651

RH122108 (e-PCR)
- UniSTS:134860

WI-11272 (e-PCR)
- UniSTS:18132

D13S1167 (e-PCR)
- UniSTS:50647

WI-17161 (e-PCR)
- UniSTS:39641

D13S128 (e-PCR)
- UniSTS:77790

RH92898 (e-PCR)
- UniSTS:92130

D13S843E (e-PCR)
- UniSTS:41445

D13S868E (e-PCR)
- UniSTS:151530

D13S871E (e-PCR)
- UniSTS:151534

NIB529 (e-PCR)
- UniSTS:55038

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cytoskeletal protein binding	IEA Inferred from Electronic Annotation more info
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables guanyl-nucleotide exchange factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Rac protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in dendrite morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in enzyme-linked receptor protein signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of skeletal muscle acetylcholine-gated channel clustering	IEA Inferred from Electronic Annotation more info
involved_in postsynaptic actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in retrograde trans-synaptic signaling by trans-synaptic protein complex	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasmic side of plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	IEA Inferred from Electronic Annotation more info
located_in extrinsic component of postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in filopodium	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: FERM, ARHGEF and pleckstrin domain-containing protein 1

Names: FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived); FERM, RhoGEF and pleckstrin domain-containing protein 1; PH domain-containing family C member 2; chondrocyte-derived ezrin-like protein; glycolysis-associated lncRNA of colorectal cancer; pleckstrin homology domain-containing family C member 2; protein phosphatase 1, regulatory subunit 75

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_001001715.4 → NP_001001715.2 FERM, ARHGEF and pleckstrin domain-containing protein 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks multiple 3' coding exons and contains an alternate 3' terminal exon, which results in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AL136300, AL445223, BM763139, BQ014327, CF994038, DB498534

Consensus CDS

CCDS32000.1

UniProtKB/Swiss-Prot

Q9Y4F1

Related

ENSP00000365765.4, ENST00000376581.9
NM_001286839.2 → NP_001273768.1 FERM, ARHGEF and pleckstrin domain-containing protein 1 isoform 3

See identical proteins and their annotated locations for NP_001273768.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and contains an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) is longer than isoform 1.

Source sequence(s)

AL136300, AL137249, AW514534, BC053593, BC071592

Consensus CDS

CCDS66572.1

UniProtKB/TrEMBL

C9JME2

Related

ENSP00000471242.1, ENST00000595437.5

Conserved Domains (9) summary

smart00295
Location:42 → 230

B41; Band 4.1 homologues

cd00160
Location:542 → 728

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

cd01220
Location:789 → 892

PH1_FARP1-like; FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 1

cd13193
Location:217 → 337

FERM_C_FARP1-like; FERM domain C-lobe of FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins

cd13235
Location:962 → 1059

PH2_FARP1-like; FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 2

pfam00169
Location:967 → 1060

PH; PH domain

pfam00373
Location:127 → 230

FERM_M; FERM central domain

pfam08736
Location:329 → 370

FA; FERM adjacent (FA)

pfam09379
Location:44 → 107

FERM_N; FERM N-terminal domain
NM_005766.4 → NP_005757.1 FERM, ARHGEF and pleckstrin domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_005757.1

Status: REVIEWED

Description

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

Source sequence(s)

AB008430, AL136300, AL137249, AW514534, BC053593, BC071592, CF994038, DB498534

Consensus CDS

CCDS9487.1

UniProtKB/Swiss-Prot

Q5JVI9, Q6IQ29, Q9Y4F1

UniProtKB/TrEMBL

A0A2X0TVY0

Related

ENSP00000322926.6, ENST00000319562.11

Conserved Domains (6) summary

smart00295
Location:42 → 230

B41; Band 4.1 homologues

cd00160
Location:542 → 728

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

cd01220
Location:753 → 861

PH1_FARP1-like; FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 1

cd13193
Location:217 → 337

FERM_C_FARP1-like; FERM domain C-lobe of FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins

cd13235
Location:931 → 1028

PH2_FARP1-like; FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 2

pfam08736
Location:329 → 370

FA; FERM adjacent (FA)