RAB11FIP3

RAB11 family interacting protein 3, the group of EF-hand domain containing|RAB11 binding domain containing

Basic information

Region (hg38): 16:425649-523011

Links

ENSG00000090565 ∙ NCBI:9727 ∙ OMIM:608738 ∙ HGNC:17224 ∙ Uniprot:O75154 ∙ 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 RAB11FIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB11FIP3 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				6	3	9
missense			49	1	1	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	49	7	4

Variants in RAB11FIP3

This is a list of pathogenic ClinVar variants found in the RAB11FIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-426025-G-C		not specified	Uncertain significance (Dec 21, 2022)
16-426031-C-T		not specified	Uncertain significance (Sep 22, 2023)
16-426050-C-T		not specified	Uncertain significance (Mar 01, 2023)
16-426086-C-G		not specified	Uncertain significance (Feb 27, 2023)
16-426096-A-G			Likely benign (Dec 31, 2019)
16-426115-G-A		not specified	Uncertain significance (May 28, 2024)
16-426120-G-A			Likely benign (Feb 25, 2018)
16-426130-G-A		not specified	Uncertain significance (Jun 28, 2022)
16-426149-C-G		not specified	Uncertain significance (Dec 18, 2023)
16-426220-G-C		not specified	Uncertain significance (May 29, 2024)
16-426227-C-T		not specified	Uncertain significance (Apr 12, 2022)
16-426229-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-426271-G-T		not specified	Uncertain significance (Mar 16, 2024)
16-426293-C-A		not specified	Uncertain significance (Mar 23, 2022)
16-426316-G-A		not specified	Uncertain significance (Jun 03, 2024)
16-426317-A-C		not specified	Uncertain significance (Sep 16, 2021)
16-426335-C-A		not specified	Uncertain significance (Aug 16, 2021)
16-426341-C-G		not specified	Uncertain significance (Oct 29, 2021)
16-426368-C-A		not specified	Uncertain significance (Dec 27, 2022)
16-426392-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-426437-G-T		not specified	Uncertain significance (Oct 04, 2022)
16-426464-G-A		not specified	Uncertain significance (Nov 27, 2023)
16-426470-G-A		not specified	Uncertain significance (May 12, 2024)
16-426493-C-G		not specified	Uncertain significance (May 03, 2023)
16-426551-C-T		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB11FIP3	protein_coding	protein_coding	ENST00000262305	14	97393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00180	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	321	392	0.820	0.0000237	4864
Missense in Polyphen		50	95.944	0.52114		1022
Synonymous	1.54	152	178	0.853	0.0000124	1512
Loss of Function	4.72	3	31.7	0.0947	0.00000145	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulator of endocytic traffic by participating in membrane delivery. Required for the abcission step in cytokinesis, possibly by acting as an 'address tag' delivering recycling endosome membranes to the cleavage furrow during late cytokinesis. Also required for the structural integrity of the endosomal recycling compartment during interphase. May play a role in breast cancer cell motility by regulating actin cytoskeleton. Acts as an adapter protein linking the dynein motor complex to various cargos and converts dynein from a non-processive to a highly processive motor in the presence of dynactin. Facilitates the interaction between dynein and dynactin and activates dynein processivity (the ability to move along a microtubule for a long distance without falling off the track) (PubMed:25035494). {ECO:0000269|PubMed:15601896, ECO:0000269|PubMed:17394487, ECO:0000269|PubMed:19327867, ECO:0000269|PubMed:25035494}.
• Pathway: Endocytosis - Homo sapiens (human);VxPx cargo-targeting to cilium;Arf6 downstream pathway;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.157
• hipred: Y
• hipred_score: 0.746
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.514

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab11fip3

Gene ontology

• Biological process: cell cycle;vesicle-mediated transport;endocytic recycling;regulation of cytokinesis;cell division;protein localization to cilium;negative regulation of adiponectin secretion
• Cellular component: nucleoplasm;endosome;centrosome;microtubule organizing center;cytosol;endocytic vesicle;midbody;cleavage furrow;intracellular membrane-bounded organelle;intercellular bridge;recycling endosome;recycling endosome membrane
• Molecular function: calcium ion binding;protein binding;Rab GTPase binding;ADP-ribosylation factor binding;protein homodimerization activity;dynein light intermediate chain binding