IFT56
intraflagellar transport 56, the group of IFT-B1 complex|Tetratricopeptide repeat domain containing
Basic information
Region (hg38): 7:139133744-139191986
Previous symbols: [ "TTC26" ]
Links
Phenotypes
GenCC
Source:
- biliary, renal, neurologic, and skeletal syndrome (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Biliary, renal, neurologic, and skeletal syndrome | AR | Cardiovascular; Endocrine; Gastrointestinal; Renal | The condition can include cardiovascular and renal anomalies, and awareness may enable early diagnosis and medical or surgical management; The condition can include pituitary insufficiency, and awareness may allow early diagnosis and management; The condition can involve hepatic dysfunction, and medical management as well as hepatic transplant may be beneficial | Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal | 31595528; 32617964; 34177428 |
| Cardiovascular |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (46 variants)
- not_provided (26 variants)
- Biliary,_renal,_neurologic,_and_skeletal_syndrome (5 variants)
- Hydrocephalus (1 variants)
- Caroli_disease (1 variants)
- IFT56-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT56 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024926.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | 3 | 9 | |||
| missense | 1 | 1 | 53 | 3 | 2 | 60 |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 3 | 5 | |||
| Total | 1 | 3 | 57 | 9 | 5 |
Highest pathogenic variant AF is 0.000006572375
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IFT56 | protein_coding | protein_coding | ENST00000464848 | 18 | 58243 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.43e-8 | 0.999 | 125705 | 0 | 43 | 125748 | 0.000171 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 226 | 290 | 0.779 | 0.0000143 | 3675 |
| Missense in Polyphen | 49 | 79.451 | 0.61673 | 1028 | ||
| Synonymous | 0.482 | 93 | 99.1 | 0.938 | 0.00000478 | 978 |
| Loss of Function | 2.91 | 19 | 38.5 | 0.494 | 0.00000203 | 456 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000635 | 0.000635 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000435 | 0.000435 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000141 | 0.000141 |
| Middle Eastern | 0.000435 | 0.000435 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the intraflagellar transport (IFT) complex B required for transport of proteins in the motile cilium. Required for transport of specific ciliary cargo proteins related to motility, while it is neither required for IFT complex B assembly or motion nor for cilium assembly. Required for efficient coupling between the accumulation of GLI2 and GLI3 at the ciliary tips and their dissociation from the negative regulator SUFU. Plays a key role in maintaining the integrity of the IFT complex B and the proper ciliary localization of the IFT complex B components. Not required for IFT complex A ciliary localization or function. Essential for maintaining proper microtubule organization within the ciliary axoneme. {ECO:0000250|UniProtKB:Q8BS45}.;
- Pathway
- Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.856
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.54
Haploinsufficiency Scores
- pHI
- 0.149
- hipred
- Y
- hipred_score
- 0.558
- ghis
- 0.541
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.256
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ttc26
- Phenotype
- cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; vision/eye phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear 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); reproductive system phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- ttc26
- Affected structure
- pronephric tubule
- Phenotype tag
- abnormal
- Phenotype quality
- distended
Gene ontology
- Biological process
- smoothened signaling pathway;axoneme assembly;intraciliary anterograde transport;intraciliary transport involved in cilium assembly;intraciliary transport;cilium assembly;protein localization to cilium;manchette assembly
- Cellular component
- centrosome;cilium;intraciliary transport particle B;motile cilium;ciliary basal body;ciliary tip;ciliary base
- Molecular function
- intraciliary transport particle B binding