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RAB40C RAB40C, member RAS oncogene family [ Homo sapiens (human) ]

Gene ID: 57799, updated on 10-Dec-2024

Summary

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Official Symbol
RAB40Cprovided by HGNC
Official Full Name
RAB40C, member RAS oncogene familyprovided by HGNC
Primary source
HGNC:HGNC:18285
See related
Ensembl:ENSG00000197562 MIM:619551; AllianceGenome:HGNC:18285
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
Also known as
RARL; RASL8C
Summary
Predicted to enable GTPase activity. Predicted to be involved in exocytosis and protein secretion. Located in Golgi apparatus and lipid droplet. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in skin (RPKM 11.6), brain (RPKM 8.2) and 25 other tissues See more
Orthologs
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Genomic context

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See RAB40C in Genome Data Viewer
Location:
16p13.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (589357..629268)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (593278..633302)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (639357..679268)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:616436-617331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:620915-621809 Neighboring gene NHL repeat containing 4 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class Q Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:633157-633913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:633914-634669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10207 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:638709-639582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6926 Neighboring gene OCT4 hESC enhancer GRCh37_chr16:649581-650082 Neighboring gene uncharacterized LOC124903618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10208 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:671701-672454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:677407-678140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:679610-680343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:680344-681078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:685245-685904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6929 Neighboring gene WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 Neighboring gene methyltransferase like 26

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. RAB40C gene polymorphisms rs62030917 and rs2269556 are associated with an increased risk of lumbar disc herniation development in the Chinese Han population. Liu K, et al. J Gene Med, 2021 Apr. PMID 32656896
  2. Rab GTPases and their roles in brain neurons and glia. Ng EL, et al. Brain Res Rev, 2008 Jun. PMID 18485483
  3. Small GTPase Rab40c associates with lipid droplets and modulates the biogenesis of lipid droplets. Tan R, et al. PLoS One, 2013. PMID 23638186, Free PMC Article
  4. Methylomics of breast cancer: Seeking epimarkers in peripheral blood of young subjects. Khakpour G, et al. Tumour Biol, 2017 Mar. PMID 28349825
  5. Rab40C is a novel Varp-binding protein that promotes proteasomal degradation of Varp in melanocytes. Yatsu A, et al. Biol Open, 2015 Feb 6. PMID 25661869, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RAB40C gene polymorphisms rs62030917 and rs2269556 are associated with an increased risk of lumbar disc herniation development in the Chinese Han population.
    Title: RAB40C gene polymorphisms rs62030917 and rs2269556 are associated with an increased risk of lumbar disc herniation development in the Chinese Han population.
  2. total of 1799 differentially methylated regions were identified including SLC6A3, Rab40C, ZNF584, and FOXD3 whose significant methylation differences were confirmed in breast cancer patients through quantitative real-time polymerase chain reaction.Methylation of those aforementioned genes in white blood cells of our young patients may highlight their potential as early epimarkers
    Title: Methylomics of breast cancer: Seeking epimarkers in peripheral blood of young subjects.
  3. Rab40c is a novel Rab protein associated with lipid droplets, and is likely involved in modulating the biogenesis of lipid droplets.
    Title: Small GTPase Rab40c associates with lipid droplets and modulates the biogenesis of lipid droplets.
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
Identification of ten loci associated with height highlights new biological pathways in human growth.
EBI GWAS Catalog
Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GDP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
colocalizes_with Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with lipid droplet IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in synaptic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ras-related protein Rab-40C
Names
RAR (RAS like GTPASE) like
RAR like
RAS-like GTPase
RAS-like, family 8, member C
SOCS box-containing protein RAR3
rar-like protein
ras-like protein family member 8C

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_001172663.2 → NP_001166134.1  ras-related protein Rab-40C isoform a

    See identical proteins and their annotated locations for NP_001166134.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1-4 all encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    BC028696, BG696681, BM677091, CX783728
    Consensus CDS
    CCDS10413.1
    UniProtKB/Swiss-Prot
    A2IDE2, D3DU54, O60795, Q4TT41, Q5PXE8, Q6PIU5, Q96S21
    UniProtKB/TrEMBL
    H3BPA5
    Related
    ENSP00000438492.1, ENST00000535977.5
    Conserved Domains (2) summary
    cd04121
    Location:9 → 281
    Rab40; Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c
    cd03742
    Location:187 → 229
    SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...

  2. NM_001172664.2 → NP_001166135.1  ras-related protein Rab-40C isoform a

    See identical proteins and their annotated locations for NP_001166135.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-4 all encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    BC028696, BG715678, BM677091
    Consensus CDS
    CCDS10413.1
    UniProtKB/Swiss-Prot
    A2IDE2, D3DU54, O60795, Q4TT41, Q5PXE8, Q6PIU5, Q96S21
    UniProtKB/TrEMBL
    H3BPA5
    Related
    ENSP00000445050.1, ENST00000539661.5
    Conserved Domains (2) summary
    cd04121
    Location:9 → 281
    Rab40; Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c
    cd03742
    Location:187 → 229
    SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...

  3. NM_001172665.2 → NP_001166136.1  ras-related protein Rab-40C isoform a

    See identical proteins and their annotated locations for NP_001166136.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1-4 all encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    BC028696, BM677091, BQ685517, BX442451, Z98883
    Consensus CDS
    CCDS10413.1
    UniProtKB/Swiss-Prot
    A2IDE2, D3DU54, O60795, Q4TT41, Q5PXE8, Q6PIU5, Q96S21
    UniProtKB/TrEMBL
    H3BPA5
    Related
    ENSP00000438382.1, ENST00000538492.5
    Conserved Domains (2) summary
    cd04121
    Location:9 → 281
    Rab40; Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c
    cd03742
    Location:187 → 229
    SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...

  4. NM_001172666.2 → NP_001166137.1  ras-related protein Rab-40C isoform b

    See identical proteins and their annotated locations for NP_001166137.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (b) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AY823398, BC028696, BM677091, BX442451, Z98883
    UniProtKB/TrEMBL
    H3BPA5
    Related
    ENSP00000455225.1, ENST00000563109.1
    Conserved Domains (2) summary
    cd03742
    Location:168 → 210
    SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...
    cl21455
    Location:9 → 262
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  5. NM_021168.5 → NP_066991.3  ras-related protein Rab-40C isoform a

    See identical proteins and their annotated locations for NP_066991.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-4 all encode the same isoform (a), which is longer than isoform b.
    Source sequence(s)
    BC028696, BM545442, BM677091, Z98883
    Consensus CDS
    CCDS10413.1
    UniProtKB/Swiss-Prot
    A2IDE2, D3DU54, O60795, Q4TT41, Q5PXE8, Q6PIU5, Q96S21
    UniProtKB/TrEMBL
    H3BPA5
    Related
    ENSP00000248139.3, ENST00000248139.8
    Conserved Domains (2) summary
    cd04121
    Location:9 → 281
    Rab40; Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c
    cd03742
    Location:187 → 229
    SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    589357..629268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    593278..633302
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96S21.1 GenPept UniProtKB/Swiss-Prot:Q96S21

Gene LinkOut

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