RAB40C

RAB40C, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 16:589357-629272

Previous symbols: [ "RASL8C" ]

Links

ENSG00000197562 ∙ NCBI:57799 ∙ OMIM:619551 ∙ HGNC:18285 ∙ Uniprot:Q96S21 ∙ 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 RAB40C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB40C 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	1	2
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	1

Variants in RAB40C

This is a list of pathogenic ClinVar variants found in the RAB40C region.

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

Position	Type	Phenotype	Significance	ClinVar
16-590302-A-G		not specified	Uncertain significance (Jun 17, 2024)
16-625438-C-A		not specified	Uncertain significance (Nov 17, 2022)
16-625985-G-A			Benign (Jan 19, 2018)
16-626043-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-626057-C-A		not specified	Uncertain significance (Nov 26, 2024)
16-626073-A-G		not specified	Uncertain significance (Feb 15, 2023)
16-626079-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-627342-T-C		not specified	Uncertain significance (Dec 06, 2021)
16-627369-G-A		not specified	Uncertain significance (Nov 25, 2024)
16-627464-G-A		not specified	Uncertain significance (May 20, 2024)
16-627509-A-T		not specified	Uncertain significance (Aug 28, 2023)
16-627524-G-A		not specified	Likely benign (Feb 06, 2023)
16-627579-G-T		not specified	Uncertain significance (Dec 17, 2021)
16-627581-C-T		not specified	Uncertain significance (Aug 11, 2022)
16-627587-C-A		not specified	Uncertain significance (Feb 21, 2024)
16-627598-G-T			Likely benign (Apr 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB40C	protein_coding	protein_coding	ENST00000535977	6	39916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0154	0.961	125647	0	5	125652	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	110	204	0.539	0.0000143	1840
Missense in Polyphen		57	107.36	0.5309		1030
Synonymous	-1.03	101	88.6	1.14	0.00000668	551
Loss of Function	1.97	5	12.5	0.399	6.20e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000481	0.0000462
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000269|PubMed:15601820}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.353
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.140
• hipred: Y
• hipred_score: 0.528
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.754

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab40c
• Phenotype: hematopoietic system 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;protein ubiquitination;Rab protein signal transduction
• Cellular component: Golgi membrane;plasma membrane;perinuclear region of cytoplasm
• Molecular function: GTPase activity;GTP binding;GDP binding