RAB11A

RAB11A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 15:65726054-65891989

Links

ENSG00000103769 ∙ NCBI:8766 ∙ OMIM:605570 ∙ HGNC:9760 ∙ Uniprot:P62491 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
• intellectual disability, autosomal dominant 56 (Strong), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB11A 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				25	4	29
missense		2	27	5	1	35
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	3	1	7
non coding				13	2	15
Total	0	2	29	43	7

Variants in RAB11A

This is a list of pathogenic ClinVar variants found in the RAB11A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65729184-C-T		not specified	Uncertain significance (Feb 08, 2023)
15-65729566-C-T		not specified	Uncertain significance (Oct 09, 2024)
15-65731663-A-G		not specified	Uncertain significance (Jan 04, 2022)
15-65731691-G-A		not specified	Uncertain significance (May 09, 2023)
15-65737776-G-C		not specified	Uncertain significance (Dec 01, 2022)
15-65737786-A-G		not specified	Uncertain significance (Feb 07, 2025)
15-65737828-T-C		not specified	Uncertain significance (Oct 09, 2024)
15-65738742-A-C		not specified	Uncertain significance (Aug 19, 2024)
15-65741772-C-T		not specified	Uncertain significance (Jan 10, 2025)
15-65752400-G-T		not specified	Uncertain significance (Nov 15, 2024)
15-65752402-C-T		not specified	Uncertain significance (May 06, 2022)
15-65752560-C-T		not specified	Uncertain significance (Aug 02, 2021)
15-65752576-T-G		not specified	Uncertain significance (Jan 04, 2022)
15-65756213-C-T		not specified	Uncertain significance (Jun 16, 2024)
15-65756315-T-C		not specified	Uncertain significance (Mar 16, 2022)
15-65756428-C-T		not specified	Uncertain significance (Feb 12, 2025)
15-65756438-T-C		not specified	Uncertain significance (Dec 17, 2023)
15-65867479-G-C			Uncertain significance (-)
15-65869595-C-T			Uncertain significance (Feb 18, 2022)
15-65869597-C-A			Likely benign (Nov 28, 2022)
15-65869601-G-C			Uncertain significance (Jul 25, 2024)
15-65869603-C-G			Uncertain significance (Apr 01, 2023)
15-65869614-A-C			Uncertain significance (Feb 12, 2024)
15-65869618-C-A			Likely benign (Dec 11, 2023)
15-65869618-C-T			Likely benign (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB11A	protein_coding	protein_coding	ENST00000261890	5	165938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00849	125729	0	1	125730	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.09	27	124	0.218	0.00000656	1411
Missense in Polyphen		5	48.82	0.10242		602
Synonymous	-0.364	43	40.1	1.07	0.00000193	418
Loss of Function	3.50	0	14.3	0.00	0.00000107	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. That Rab regulates endocytic recycling. Acts as a major regulator of membrane delivery during cytokinesis. Together with MYO5B and RAB8A participates in epithelial cell polarization. Together with RAB3IP, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. Together with MYO5B participates in CFTR trafficking to the plasma membrane and TF (Transferrin) recycling in nonpolarized cells. Required in a complex with MYO5B and RAB11FIP2 for the transport of NPC1L1 to the plasma membrane. Participates in the sorting and basolateral transport of CDH1 from the Golgi apparatus to the plasma membrane. Regulates the recycling of FCGRT (receptor of Fc region of monomeric Ig G) to basolateral membranes. May also play a role in melanosome transport and release from melanocytes. {ECO:0000269|PubMed:15601896, ECO:0000269|PubMed:15689490, ECO:0000269|PubMed:17462998, ECO:0000269|PubMed:19542231, ECO:0000269|PubMed:20890297, ECO:0000269|PubMed:21282656}.
• Pathway: Endocytosis - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);NOTCH-Ncore;VEGFA-VEGFR2 Signaling Pathway;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Fibroblast growth factor-1;Rab regulation of trafficking;Thromboxane A2 receptor signaling;Notch signaling pathway;RAB geranylgeranylation;Anchoring of the basal body to the plasma membrane;VxPx cargo-targeting to cilium;Arf6 downstream pathway;IL8- and CXCR2-mediated signaling events;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.260

Intolerance Scores

• loftool: 0.173
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.478
• hipred: Y
• hipred_score: 0.749
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab11a
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; immune system phenotype; cellular 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); digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: rab11a
• Affected structure: vasculature
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: renal water homeostasis;intracellular protein transport;exocytosis;mitotic metaphase plate congression;positive regulation of epithelial cell migration;regulation of multivesicular body size;positive regulation of G2/M transition of mitotic cell cycle;vesicle-mediated transport;astral microtubule organization;neuron projection development;melanosome transport;regulation of cytokinesis;Rab protein signal transduction;multivesicular body assembly;post-translational protein modification;positive regulation of axon extension;regulation of long-term neuronal synaptic plasticity;plasma membrane to endosome transport;regulation of protein transport;establishment of vesicle localization;regulation of vesicle-mediated transport;establishment of protein localization to organelle;protein localization to plasma membrane;establishment of protein localization to membrane;mitotic spindle assembly;ciliary basal body-plasma membrane docking;neurotransmitter receptor transport, endosome to postsynaptic membrane;vesicle-mediated transport in synapse;positive regulation of protein localization to plasma membrane;exosomal secretion
• Cellular component: spindle pole;endosome;multivesicular body;Golgi apparatus;trans-Golgi network;centrosome;microtubule organizing center;kinetochore microtubule;cytosol;transport vesicle;axon;cytoplasmic vesicle membrane;cytoplasmic vesicle;vesicle;cleavage furrow;protein-containing complex;intracellular membrane-bounded organelle;phagocytic vesicle;perinuclear region of cytoplasm;recycling endosome;recycling endosome membrane;extracellular exosome;Schaffer collateral - CA1 synapse;postsynaptic recycling endosome;glutamatergic synapse
• Molecular function: GTPase activity;protein binding;GTP binding;microtubule binding;syntaxin binding;myosin V binding