RAB11FIP3

protein-coding

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

Gene summary

Proteins of the large Rab GTPase family (see RAB1A; MIM 179508) have regulatory roles in the formation, targeting, and fusion of intracellular transport vesicles. RAB11FIP3 is one of many proteins that interact with and regulate Rab GTPases (Hales et al., 2001 [PubMed 11495908]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_014700.4

Inheritance

—

ClinVar variants

U:139B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr16:425,649-523,011

External References & Databases

Ensembl (ENSG00000090565)

Transcript & Mutation Effects

hg38 • Region Span ~97.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAB11FIP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014700.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	6 clinvar	3 clinvar	11
missense			134 clinvar	4 clinvar	1 clinvar	139
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	139	10	4	153

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014700.4	RefSeq	NP_055515.1	14	MANE Select
ENST00000262305.9	Ensembl	ENSP00000262305.4	14	MANE Select
NM_001142272.2	RefSeq	NP_001135744.2	11	Standard
NM_001370401.1	RefSeq	NP_001357330.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)
VxPx cargo-targeting to cilium
Arf6 downstream pathway
Cargo trafficking to the periciliary membrane
Cilium Assembly

Biological Process

cell cycle
vesicle-mediated transport
endocytic recycling
regulation of cytokinesis
cell division

Molecular Function

calcium ion binding
protein binding
Rab GTPase binding
ADP-ribosylation factor binding
protein homodimerization activity

Cellular Component

nucleoplasm
endosome
centrosome
microtubule organizing center
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262305
Coding exons: 14
Length: 97393
Individuals with no LoFs: 125745
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125748
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	321	392	0.820	0.0000237	4864
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.109

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.514

Gene Damage Prediction

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