RAB29

RAB29, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 1:205767986-205775482

Previous symbols: [ "RAB7L", "RAB7L1" ]

Links

ENSG00000117280 ∙ NCBI:8934 ∙ OMIM:603949 ∙ HGNC:9789 ∙ Uniprot:O14966 ∙ 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 RAB29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB29 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		1	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	10	0	1

Variants in RAB29

This is a list of pathogenic ClinVar variants found in the RAB29 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205770409-A-G		not specified	Uncertain significance (Jun 16, 2024)
1-205770415-T-A		not specified	Uncertain significance (Mar 20, 2024)
1-205770427-T-A		not specified	Uncertain significance (Mar 17, 2023)
1-205770779-T-G		not specified	Uncertain significance (Aug 17, 2021)
1-205770794-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-205770811-C-T		not specified	Uncertain significance (Mar 05, 2024)
1-205770812-G-A		not specified	Uncertain significance (Nov 11, 2024)
1-205770812-G-C		not specified	Uncertain significance (Aug 16, 2021)
1-205770827-G-C		not specified	Uncertain significance (May 06, 2022)
1-205770838-C-A		not specified	Uncertain significance (Dec 26, 2023)
1-205771483-A-G		RAB29-related disorder	Likely benign (Mar 27, 2024)
1-205771540-G-C		RAB29-related disorder	Benign (Jun 21, 2019)
1-205771608-G-A		not specified	Uncertain significance (Nov 24, 2024)
1-205771617-T-C		not specified	Uncertain significance (Aug 14, 2024)
1-205771626-C-T		not specified	Uncertain significance (Mar 28, 2023)
1-205772499-C-A		not specified	Uncertain significance (Apr 17, 2023)
1-205772519-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-205774850-T-A		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB29	protein_coding	protein_coding	ENST00000367139	5	7475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.182	0.808	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	76	116	0.657	0.00000620	1343
Missense in Polyphen		26	45.808	0.56758		557
Synonymous	0.527	40	44.5	0.899	0.00000235	380
Loss of Function	2.20	3	10.8	0.278	5.61e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab GTPase key regulator in vesicle trafficking. Essential for maintaining the integrity of the endosome-trans- Golgi network structure. Together with LRRK2, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner. Regulates neuronal process morphology in the intact central nervous system (CNS). May play a role in the formation of typhoid toxin transport intermediates during Salmonella enterica serovar Typhi (S.Typhi) epithelial cell infection. {ECO:0000269|PubMed:22042847, ECO:0000269|PubMed:24788816}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.580
• ghis: 0.581

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rab29

Gene ontology

• Biological process: positive regulation of receptor recycling;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;mitochondrion organization;Golgi organization;synapse assembly;response to bacterium;negative regulation of neuron projection development;Rab protein signal transduction;viral RNA genome replication;T cell activation;retrograde transport, endosome to Golgi;positive regulation of T cell receptor signaling pathway;protein localization to membrane;positive regulation of intracellular protein transport;regulation of neuron death;protein localization to ciliary membrane;regulation of retrograde transport, endosome to Golgi;multi-organism toxin transport
• Cellular component: cytoplasm;mitochondrion;early endosome;vacuole;Golgi apparatus;cis-Golgi network;trans-Golgi network;cytosol;cytoskeleton;plasma membrane;symbiont-containing vacuole;melanosome;perinuclear region of cytoplasm;recycling endosome;extracellular exosome;intracellular vesicle
• Molecular function: GTPase activity;protein binding;GTP binding;Rab GTPase binding;GDP binding;kinesin binding;dynein complex binding