RAB5C

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

Basic information

Region (hg38): 17:42124978-42155044

Previous symbols: [ "RABL" ]

Links

ENSG00000108774

∙ NCBI:5878 ∙ OMIM:604037 ∙ HGNC:9785 ∙ Uniprot:P51148 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB5C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB5C gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1 clinvar	1
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in RAB5C

This is a list of pathogenic ClinVar variants found in the RAB5C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
17-42125815-G-A	Inborn genetic diseases	Uncertain significance (May 27, 2022)	2292104
17-42125841-C-T	Inborn genetic diseases	Uncertain significance (Feb 21, 2024)	3150820
17-42125877-T-A	Inborn genetic diseases	Uncertain significance (Sep 07, 2022)	2311340
17-42126785-T-C	Inborn genetic diseases	Uncertain significance (Jun 04, 2024)	3312203
17-42128273-G-A		Benign (May 05, 2020)	1241743
17-42128308-C-T	Inborn genetic diseases	Uncertain significance (Dec 11, 2023)	3150818
17-42128365-T-G	Inborn genetic diseases	Uncertain significance (Aug 15, 2023)	2618690
17-42128665-T-C	Inborn genetic diseases	Uncertain significance (Feb 16, 2023)	2486477
17-42128728-T-C	RAB5C-related disorder • Inborn genetic diseases	Uncertain significance (Oct 26, 2022)	1342146
17-42128777-A-C	Inborn genetic diseases	Uncertain significance (Nov 15, 2023)	3150816
17-42130483-G-A	Inborn genetic diseases	Uncertain significance (Jul 27, 2021)	2239682
17-42130484-C-T	Inborn genetic diseases	Uncertain significance (May 05, 2023)	2523312
17-42130499-C-T	Inborn genetic diseases	Uncertain significance (Dec 13, 2023)	3150819

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB5C	protein_coding	protein_coding	ENST00000547517	6	30042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.937	0.0628	124987	0	1	124988	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	98	146	0.670	0.00000876	1615
Missense in Polyphen		7	36.958	0.18941		470
Synonymous	0.251	54	56.4	0.958	0.00000367	487
Loss of Function	3.11	1	13.2	0.0758	8.29e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity). {ECO:0000250}.;
Pathway: Endocytosis - Homo sapiens (human);Phagosome - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Ras Signaling;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Clathrin-mediated endocytosis;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation (Consensus)

Recessive Scores

pRec: 0.130

Intolerance Scores

loftool: 0.793
rvis_EVS: 0.22
rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

pHI: 0.578
hipred: Y
hipred_score: 0.749
ghis: 0.411

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.988

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Rab5c
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name: rab5c
Affected structure: skeletal muscle
Phenotype tag: abnormal
Phenotype quality: disorganized

Gene ontology

Biological process: intracellular protein transport;regulation of endocytosis;Rab protein signal transduction;neutrophil degranulation;plasma membrane to endosome transport
Cellular component: lysosomal membrane;endosome;early endosome;lipid droplet;plasma membrane;endocytic vesicle;early endosome membrane;azurophil granule membrane;melanosome;extracellular exosome
Molecular function: GTPase activity;protein binding;GTP binding;GDP binding