RAB4A

RAB4A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 1:229271062-229305894

Previous symbols: [ "RAB4" ]

Links

ENSG00000168118 ∙ NCBI:5867 ∙ OMIM:179511 ∙ HGNC:9781 ∙ Uniprot:P20338 ∙ 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 RAB4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB4A 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	11	1	0

Variants in RAB4A

This is a list of pathogenic ClinVar variants found in the RAB4A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-229288767-G-A		not specified	Uncertain significance (Jan 25, 2023)
1-229288788-G-T		not specified	Uncertain significance (May 12, 2024)
1-229288800-G-A		not specified	Uncertain significance (Nov 10, 2022)
1-229297538-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-229297591-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-229299018-G-A		not specified	Uncertain significance (Apr 13, 2023)
1-229299021-G-C		not specified	Uncertain significance (Feb 27, 2023)
1-229302939-C-G		not specified	Uncertain significance (Aug 21, 2023)
1-229302939-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-229302949-C-T		not specified	Uncertain significance (May 03, 2023)
1-229302958-C-G		not specified	Uncertain significance (Oct 21, 2021)
1-229305153-T-C		not specified	Likely benign (Aug 02, 2021)
1-229305231-G-A		not specified	Uncertain significance (Jun 17, 2024)
1-229305234-A-G		not specified	Uncertain significance (May 12, 2024)
1-229305246-G-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB4A	protein_coding	protein_coding	ENST00000366690	7	34820

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.203	0.796	125725	0	19	125744	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	84	124	0.676	0.00000736	1414
Missense in Polyphen		26	41.982	0.61931		476
Synonymous	-0.369	51	47.8	1.07	0.00000329	406
Loss of Function	2.71	4	15.5	0.258	0.00000101	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000414	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000634	0.0000615
Middle Eastern	0.000414	0.000381
South Asian	0.0000333	0.0000327
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);VEGFA-VEGFR2 Signaling Pathway;Insulin Signaling;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;Metabolism;Rab regulation of trafficking;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;RAB geranylgeranylation;Translocation of GLUT4 to the plasma membrane;PDGFR-beta signaling pathway (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.435
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.792
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab4a

Zebrafish Information Network

• Gene name: rab4a
• Affected structure: vasculature
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;intracellular protein transport;antigen processing and presentation;regulation of endocytosis;Rab protein signal transduction;positive regulation of ATPase activity
• Cellular component: endosome;cytosol;plasma membrane;cytoplasmic vesicle membrane;early endosome membrane;vesicle;insulin-responsive compartment;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;recycling endosome membrane;extracellular exosome;postsynaptic recycling endosome;anchored component of synaptic vesicle membrane
• Molecular function: ATPase activator activity;GTPase activity;protein binding;GTP binding;protein transporter activity;GDP binding;syntaxin binding;ionotropic glutamate receptor binding;ATPase binding