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ARHGEF38 Rho guanine nucleotide exchange factor 38 [ Homo sapiens (human) ]

Gene ID: 54848, updated on 2-Nov-2024

Summary

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Official Symbol
ARHGEF38provided by HGNC
Official Full Name
Rho guanine nucleotide exchange factor 38provided by HGNC
Primary source
HGNC:HGNC:25968
See related
Ensembl:ENSG00000236699 MIM:619919; AllianceGenome:HGNC:25968
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in prostate (RPKM 3.4), colon (RPKM 1.7) and 11 other tissues See more
Orthologs
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Genomic context

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See ARHGEF38 in Genome Data Viewer
Location:
4q24
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (105552620..105682566)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (108863418..108993730)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (106473777..106602071)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377352 Neighboring gene ATP synthase F1 subunit epsilon pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:106476385-106476934 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:106477486-106478035 Neighboring gene ARHGEF38 intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21783 Neighboring gene integrator complex subunit 12 Neighboring gene uncharacterized LOC124900748 Neighboring gene uncharacterized LOC124900747

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Lansdon LA, et al. Am J Hum Genet, 2023 Jan 5. PMID 36493769, Free PMC Article
  2. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Hancock DB, et al. Nat Genet, 2010 Jan. PMID 20010835, Free PMC Article
  3. Gene network analysis in a pediatric cohort identifies novel lung function genes. Ong BA, et al. PLoS One, 2013. PMID 24023788, Free PMC Article
  4. Mutation of ARHGAP9 in patients with coronary spastic angina. Takefuji M, et al. J Hum Genet, 2010 Jan. PMID 19911011
  5. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. Kalsi G, et al. Hum Mol Genet, 2010 Jun 15. PMID 20332099, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes.
    Title: Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes.
  2. 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.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
  4. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
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
Gene network analysis in a pediatric cohort identifies novel lung function genes.
EBI GWAS Catalog
Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20184, FLJ43963

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
rho guanine nucleotide exchange factor 38
Names
Rho guanine nucleotide exchange factor (GEF) 38

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)

  1. NM_001242729.2 → NP_001229658.1  rho guanine nucleotide exchange factor 38 isoform 1

    See identical proteins and their annotated locations for NP_001229658.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC105391, AK000191, AK125951, DT932593
    Consensus CDS
    CCDS56338.1
    UniProtKB/Swiss-Prot
    C9JIB4, Q9NXL2
    Related
    ENSP00000416125.2, ENST00000420470.3
    Conserved Domains (4) summary
    cd07589
    Location:336 → 522
    BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein
    cd12141
    Location:717 → 773
    SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains
    pfam00621
    Location:98 → 284
    RhoGEF; RhoGEF domain
    cl17036
    Location:586 → 642
    SH3; Src Homology 3 domain superfamily

  2. NM_017700.2 → NP_060170.1  rho guanine nucleotide exchange factor 38 isoform 2

    See identical proteins and their annotated locations for NP_060170.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents an alternate 3' splice pattern with a shorter coding region, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK000191
    Consensus CDS
    CCDS3670.1
    UniProtKB/Swiss-Prot
    Q9NXL2
    Related
    ENSP00000265154.2, ENST00000265154.6
    Conserved Domains (1) summary
    cl02571
    Location:98 → 194
    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.

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

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    105552620..105682566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532050.3 → XP_011530352.1  rho guanine nucleotide exchange factor 38 isoform X1

    Conserved Domains (4) summary
    cd07589
    Location:171 → 357
    BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein
    cd12141
    Location:552 → 608
    SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains
    cl02571
    Location:4 → 119
    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.
    cl17036
    Location:421 → 477
    SH3; Src Homology 3 domain superfamily

  2. XM_011532051.3 → XP_011530353.1  rho guanine nucleotide exchange factor 38 isoform X3

    Conserved Domains (2) summary
    pfam00621
    Location:98 → 284
    RhoGEF; RhoGEF domain
    cl12013
    Location:336 → 419
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  3. XM_006714244.4 → XP_006714307.1  rho guanine nucleotide exchange factor 38 isoform X2

    Conserved Domains (4) summary
    cd07589
    Location:118 → 304
    BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein
    cd12141
    Location:499 → 555
    SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains
    cl02571
    Location:1 → 66
    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.
    cl17036
    Location:368 → 424
    SH3; Src Homology 3 domain superfamily

RNA

  1. XR_938749.4 RNA Sequence

  2. XR_007057934.1 RNA Sequence

  3. XR_938750.4 RNA Sequence

  4. XR_001741247.3 RNA Sequence

  5. XR_938751.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    108863418..108993730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350283.1 → XP_054206258.1  rho guanine nucleotide exchange factor 38 isoform X1

  2. XM_054350285.1 → XP_054206260.1  rho guanine nucleotide exchange factor 38 isoform X3

  3. XM_054350284.1 → XP_054206259.1  rho guanine nucleotide exchange factor 38 isoform X2

RNA

  1. XR_008486996.1 RNA Sequence

  2. XR_008486998.1 RNA Sequence

  3. XR_008486999.1 RNA Sequence

  4. XR_008486997.1 RNA Sequence

  5. XR_008487000.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXL2.2 GenPept UniProtKB/Swiss-Prot:Q9NXL2

Gene LinkOut

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