RAB11FIP4

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

Basic information

Region (hg38): 17:31391675-31538211

Links

ENSG00000131242 ∙ NCBI:84440 ∙ OMIM:611999 ∙ HGNC:30267 ∙ Uniprot:Q86YS3 ∙ 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 RAB11FIP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB11FIP4 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in RAB11FIP4

This is a list of pathogenic ClinVar variants found in the RAB11FIP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-31391874-T-G		not specified	Likely benign (Apr 07, 2023)
17-31391883-C-T		not specified	Uncertain significance (Mar 29, 2022)
17-31391916-C-T		not specified	Uncertain significance (Aug 17, 2022)
17-31391945-C-G		not specified	Uncertain significance (Oct 26, 2021)
17-31391955-T-C		not specified	Uncertain significance (Mar 28, 2024)
17-31391979-G-A		not specified	Uncertain significance (Apr 13, 2022)
17-31391979-G-T		not specified	Uncertain significance (Apr 24, 2024)
17-31434075-G-A		not specified	Uncertain significance (Oct 30, 2023)
17-31434082-C-T		not specified	Uncertain significance (Mar 16, 2022)
17-31517657-G-A		not specified	Uncertain significance (Feb 07, 2023)
17-31517725-C-A		not specified	Uncertain significance (Nov 08, 2022)
17-31517822-G-A		not specified	Uncertain significance (Oct 14, 2023)
17-31517822-G-T		not specified	Uncertain significance (Dec 15, 2022)
17-31517834-G-A		not specified	Uncertain significance (Oct 06, 2023)
17-31521212-C-T		not specified	Uncertain significance (Apr 23, 2024)
17-31521234-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-31521275-G-A		not specified	Uncertain significance (May 12, 2024)
17-31521333-C-T		not specified	Uncertain significance (Apr 09, 2024)
17-31521986-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-31525131-C-T		not specified	Uncertain significance (Aug 30, 2022)
17-31525142-G-T		not specified	Uncertain significance (Jul 13, 2022)
17-31525185-A-G		not specified	Uncertain significance (Aug 22, 2023)
17-31525194-G-A		not specified	Uncertain significance (Apr 20, 2023)
17-31527859-A-G		not specified	Uncertain significance (Sep 01, 2021)
17-31528415-C-T		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB11FIP4	protein_coding	protein_coding	ENST00000325874	15	146595

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00801	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.49	241	377	0.639	0.0000239	4168
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

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. 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}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.0285
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

• pHI: 0.162
• hipred: Y
• hipred_score: 0.806
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab11fip4

Zebrafish Information Network

• Gene name: rab11fip4a
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: neural retina development;viral process;endocytic recycling;regulation of cytokinesis;positive regulation of G1 to G0 transition
• Cellular component: extracellular space;endosome;centrosome;spindle;endocytic vesicle;midbody;cleavage furrow;perinuclear region of cytoplasm;recycling endosome membrane
• Molecular function: calcium ion binding;protein binding;Rab GTPase binding;ADP-ribosylation factor binding;protein homodimerization activity