GeneBe

RAB5C

protein-coding

RAB5C, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Gene summary

Members of the Rab protein family are small GTPases of the Ras superfamily that are thought to ensure fidelity in the process of docking and/or fusion of vesicles with their correct acceptor compartment (Han et al., 1996 [PubMed 8646882]).[supplied by OMIM, Nov 2010]

Previous symbols:
  • RABL

MANE transcript

NM_004583.4

Inheritance

AD

ClinVar variants

P:2U:32B:1

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr17:42,124,978-42,155,044

External References & Databases

Ensembl (ENSG00000108774)NCBI Gene (5878)OMIM (604037)HGNC:9785GenCCUniProt (P51148)AlphaFoldClinVar (RAB5C)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~30.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: G2P

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAB5C variants in ClinVar

7 Conditions Cataloged
Inborn genetic diseasesTotal: 22
not providedTotal: 4
RAB5C-related disorderTotal: 4
RAB5C-related developmental disorderTotal: 1
RAB5C-associated macrocephaly and developmental delayTotal: 1
Macrocephaly-developmental delay syndromeTotal: 1
RAB5C-related neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004583.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
2
clinvar
27
clinvar
1
clinvar
 30
nonsense
1
clinvar
 1
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
0
Total02321035
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004583.4RefSeqNP_004574.25MANE Select
ENST00000346213.9EnsemblENSP00000345689.55MANE Select
NM_001252039.2RefSeqNP_001238968.16Standard
NM_201434.3RefSeqNP_958842.15Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
rab5cDanio rerio

Structure: skeletal muscle

Quality: disorganized

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Endocytosis - Homo sapiens (human)
  • Phagosome - Homo sapiens (human)
  • Vasopressin-regulated water reabsorption - Homo sapiens (human)
  • Amoebiasis - Homo sapiens (human)
  • Tuberculosis - Homo sapiens (human)

Biological Process

  • intracellular protein transport
  • regulation of endocytosis
  • Rab protein signal transduction
  • neutrophil degranulation
  • plasma membrane to endosome transport

Molecular Function

  • GTPase activity
  • protein binding
  • GTP binding
  • GDP binding

Cellular Component

  • lysosomal membrane
  • endosome
  • early endosome
  • lipid droplet
  • plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000547517
Coding exons
6
Length
30042
Individuals with no LoFs
124987
Homozygous LoFs
0
Heterozygous LoFs
1
Defined
124988
p
0.00000400
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.42981460.6700.000008761615
Missense (PolyPhen)736.9580.18941470
Synonymous0.2515456.40.9580.00000367487
Loss of Function3.11113.20.07588.29e-7131

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000550.000055rare
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity). {ECO:0000250}.;

Recessive Scores

pRec
0.130

Intolerance Scores

LoFtool
0.793
RVIS EVS
0.22
RVIS percentile EVS
67.92

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.988

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.