IFT46

intraflagellar transport 46, the group of Cilia and flagella associated|IFT-B1 complex

Basic information

Region (hg38): 11:118544528-118572970

Previous symbols: [ "C11orf60" ]

Links

ENSG00000118096 ∙ NCBI:56912 ∙ ∙ HGNC:26146 ∙ Uniprot:Q9NQC8 ∙ 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 IFT46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT46 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	13	2	0

Variants in IFT46

This is a list of pathogenic ClinVar variants found in the IFT46 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118544927-T-C		not specified	Uncertain significance (Mar 07, 2024)
11-118544962-T-C		not specified	Uncertain significance (Nov 10, 2022)
11-118544971-G-A		not specified	Uncertain significance (Mar 16, 2024)
11-118544995-G-C		not specified	Uncertain significance (Oct 07, 2024)
11-118545421-G-C		not specified	Uncertain significance (Mar 31, 2023)
11-118545464-C-T		not specified	Uncertain significance (Sep 17, 2021)
11-118545802-T-C		not specified	Uncertain significance (Mar 23, 2023)
11-118545817-C-T		not specified	Uncertain significance (Jan 26, 2023)
11-118551797-G-A		not specified	Uncertain significance (Oct 29, 2024)
11-118551811-G-A		not specified	Uncertain significance (Apr 07, 2022)
11-118551845-G-A		not specified	Uncertain significance (Sep 27, 2024)
11-118552248-G-A		not specified	Uncertain significance (Aug 28, 2024)
11-118552250-T-C		not specified	Uncertain significance (Nov 15, 2021)
11-118552267-C-G		not specified	Uncertain significance (Nov 10, 2024)
11-118552277-G-A		not specified	Likely benign (Feb 17, 2022)
11-118555036-A-C		not specified	Uncertain significance (Sep 14, 2021)
11-118555043-G-C			Likely benign (Nov 01, 2022)
11-118555081-T-C		not specified	Uncertain significance (Dec 05, 2024)
11-118555083-C-T		not specified	Likely benign (Oct 01, 2024)
11-118555251-C-T		not specified	Uncertain significance (Dec 21, 2022)
11-118555317-T-C		not specified	Uncertain significance (Sep 17, 2021)
11-118557018-G-T		not specified	Uncertain significance (Nov 18, 2023)
11-118557049-T-C			Benign (Apr 20, 2018)
11-118557832-A-T		not specified	Uncertain significance (May 11, 2022)
11-118572348-G-C			Benign (May 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT46	protein_coding	protein_coding	ENST00000264020	11	28443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.168	0.831	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.673	166	192	0.863	0.00000964	2364
Missense in Polyphen		43	53.24	0.80767		682
Synonymous	1.72	54	72.6	0.744	0.00000388	630
Loss of Function	3.02	5	19.3	0.259	8.16e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000664	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia. May play a role in chondrocyte maturation and skeletogenesis (By similarity). {ECO:0000250}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0887

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.0945
• hipred: Y
• hipred_score: 0.530
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ift46
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: ift46
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: smoothened signaling pathway;biological_process;intraciliary transport involved in cilium assembly;intraciliary transport;protein stabilization;cilium assembly
• Cellular component: cytoplasm;centrosome;cilium;intraciliary transport particle B;motile cilium;ciliary basal body;ciliary tip
• Molecular function: molecular_function;protein C-terminus binding