RAB11FIP4

protein-coding

RAB11 family interacting protein 4, the group of EF-hand domain containing|MicroRNA protein coding host genes|RAB11 binding domain containing

Gene summary

The protein encoded by this gene interacts with RAB11 and is thought to be involved in bringing recycling endosome membranes to the cleavage furrow in late cytokinesis. Hypoxic conditions can lead to an upregulation of the encoded protein and enhance the metastatic potential of hepatocellular carcinoma. [provided by RefSeq, Oct 2016]

MANE transcript

NM_032932.6

Inheritance

—

ClinVar variants

U:102B:1

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr17:31,391,675-31,538,211

External References & Databases

Ensembl (ENSG00000131242)

Transcript & Mutation Effects

hg38 • Region Span ~146.5 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 RAB11FIP4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 90

Prostate cancerTotal: 1

RAB11FIP4-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032932.6. 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			5 clinvar			5
missense			92 clinvar	1 clinvar		93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	102	1	0	103

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032932.6	RefSeq	NP_116321.2	15	MANE Select
ENST00000621161.5	Ensembl	ENSP00000482620.1	15	MANE Select
NM_001303542.3	RefSeq	NP_001290471.2	13	Standard
NM_001346747.2	RefSeq	NP_001333676.1	12	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rab11fip4a	Danio rerio	Structure: retinal ganglion cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

rab11fip4a

Danio rerio

Structure: retinal ganglion cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)

Biological Process

neural retina development
viral process
endocytic recycling
regulation of cytokinesis
positive regulation of G1 to G0 transition

Molecular Function

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

Cellular Component

extracellular space
endosome
centrosome
spindle
endocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325874
Coding exons: 15
Length: 146595
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125747
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.49	241	377	0.639	0.0000239	4168
Missense (PolyPhen)		75	142.79	0.52524		1458
Synonymous	-0.132	165	163	1.01	0.0000112	1204
Loss of Function	4.59	4	32.1	0.125	0.00000162	371

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

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. In case of infection by HCMV (human cytomegalovirus), may participate in egress of the virus out of nucleus; this function is independent of ARF6. {ECO:0000269|PubMed:12470645}.;

Recessive Scores

pRec: 0.123

Intolerance Scores

LoFtool: 0.0285
RVIS EVS: -0.87
RVIS percentile EVS: 10.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.796

Gene Damage Prediction

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