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

Summary

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 GDP binding activity; GTP binding activity; and GTPase activity. Predicted to be involved in protein localization to plasma membrane. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in endosome; plasma membrane; and synaptic vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in skin (RPKM 11.6), brain (RPKM 8.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (589357..629268)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (593278..633302)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (639357..679268)

Chromosome 16 - NC_000016.10 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?

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.
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.
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.

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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 EBI GWAS CatalogPubMed
Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects. 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

A009L31 (e-PCR)
- UniSTS:29001

RH104058 (e-PCR)
- UniSTS:98383

RAB40C_1470 (e-PCR)
- UniSTS:277645

RAB40C_v500 (e-PCR)
- UniSTS:277645

SHGC-60694 (e-PCR)
- UniSTS:22236

G32656 (e-PCR)
- UniSTS:117238

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 secretion	IBA Inferred from Biological aspect of Ancestor 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)

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 ...
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 ...
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 ...
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
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 ...