RAB6C

RAB6C, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 2:129979666-129982738

Links

ENSG00000222014 ∙ NCBI:84084 ∙ OMIM:612909 ∙ HGNC:16525 ∙ Uniprot:Q9H0N0 ∙ 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 RAB6C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB6C 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						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in RAB6C

This is a list of pathogenic ClinVar variants found in the RAB6C region.

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

Position	Type	Phenotype	Significance	ClinVar
2-129980136-C-A		not specified	Uncertain significance (Oct 02, 2023)
2-129980146-C-G		not specified	Uncertain significance (May 01, 2024)
2-129980335-C-T		not specified	Uncertain significance (Mar 31, 2023)
2-129980339-T-A		not specified	Uncertain significance (Jan 09, 2024)
2-129980362-A-C		not specified	Uncertain significance (Apr 15, 2024)
2-129980392-T-G		not specified	Uncertain significance (Feb 17, 2023)
2-129980407-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-129980422-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-129980525-C-T		not specified	Uncertain significance (May 10, 2022)
2-129980527-G-A		not specified	Uncertain significance (Sep 14, 2022)
2-129980561-A-G		not specified	Uncertain significance (Dec 18, 2023)
2-129980567-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-129980582-G-A		not specified	Uncertain significance (Oct 25, 2023)
2-129980618-G-A		not specified	Uncertain significance (Aug 16, 2022)
2-129980632-G-A		not specified	Uncertain significance (Apr 22, 2022)
2-129980725-G-C		not specified	Uncertain significance (Jul 15, 2021)
2-129980767-C-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB6C	protein_coding	protein_coding	ENST00000410061	1	3077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	128	131	0.975	0.00000597	1626
Missense in Polyphen		38	40.129	0.94694		527
Synonymous	0.114	51	52.0	0.980	0.00000250	511
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of centrosome duplication and cell cycle progression. {ECO:0000269|PubMed:17426708, ECO:0000269|PubMed:18992151, ECO:0000269|PubMed:20064528}.

Recessive Scores

• pRec: 0.0289

Intolerance Scores

• loftool: 0.722
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.23

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Gene ontology

• Biological process: mitotic cell cycle;intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;small GTPase mediated signal transduction;regulation of centrosome duplication;Rab protein signal transduction;retrograde transport, endosome to Golgi;response to drug
• Cellular component: nucleus;Golgi apparatus;centrosome;cytosol
• Molecular function: GTPase activity;GTP binding