RAB40A

RAB40A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): X:103499130-103519489

Links

ENSG00000172476 ∙ NCBI:142684 ∙ OMIM:301065 ∙ HGNC:18283 ∙ Uniprot:Q8WXH6 ∙ 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 RAB40A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB40A 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in RAB40A

This is a list of pathogenic ClinVar variants found in the RAB40A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-103499944-T-G		not specified	Uncertain significance (Mar 30, 2024)
X-103499988-C-T		not specified	Uncertain significance (Jul 31, 2024)
X-103500023-G-C		not specified	Uncertain significance (Jun 01, 2023)
X-103500108-T-C		not specified	Likely benign (Nov 22, 2021)
X-103500110-C-A		not specified	Likely benign (Nov 22, 2021)
X-103500216-T-A		not specified	Uncertain significance (Jan 16, 2025)
X-103500254-G-A		not specified	Uncertain significance (Feb 14, 2023)
X-103500257-A-G		not specified	Uncertain significance (May 10, 2022)
X-103500324-C-G		not specified	Uncertain significance (Apr 04, 2024)
X-103500371-T-A		not specified	Uncertain significance (Jun 11, 2024)
X-103500389-A-C		not specified	Uncertain significance (Feb 17, 2022)
X-103500416-T-C		not specified	Uncertain significance (Jun 04, 2024)
X-103500447-C-T		not specified	Uncertain significance (Aug 15, 2023)
X-103500461-C-A		not specified	Uncertain significance (Sep 18, 2024)
X-103500500-C-A		not specified	Uncertain significance (Jan 17, 2024)
X-103500501-C-T		not specified	Uncertain significance (Feb 05, 2024)
X-103500545-G-A		not specified	Uncertain significance (Jan 25, 2023)
X-103500548-G-A		not specified	Uncertain significance (Oct 26, 2021)
X-103500558-G-T		not specified	Uncertain significance (Apr 17, 2023)
X-103500565-C-G		not specified	Uncertain significance (Mar 19, 2024)
X-103500594-T-C		not specified	Uncertain significance (Dec 17, 2023)
X-103500632-G-A			Uncertain significance (-)
X-103500647-C-T		not specified	Uncertain significance (Mar 08, 2025)
X-103500696-C-T		not specified	Uncertain significance (May 11, 2022)
X-103500698-A-G		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB40A	protein_coding	protein_coding	ENST00000372633	1	19740

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	0.792	100	125	0.801	0.0000107	1805
Missense in Polyphen		41	57.703	0.71053		780
Synonymous	1.22	43	54.4	0.790	0.00000490	570
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 a 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:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.612
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.35

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.187
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Gene ontology

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