IFT56
protein-codingintraflagellar transport 56, the group of IFT-B1 complex|Tetratricopeptide repeat domain containing
Gene summary
Predicted to enable intraciliary transport particle B binding activity. Involved in cilium assembly. Located in cilium. Part of intraciliary transport particle A. [provided by Alliance of Genome Resources, Jun 2026]
- TTC26
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~58.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0859191
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0859191
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal
Intervention: Cardiovascular; Endocrine; Gastrointestinal; Renal
Rationale: 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
Comments: Cardiovascular
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to IFT56 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024926.4. 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 | 1 | 29 | 3 | 33 | ||
| missense | 1 | 1 | 64 | 7 | 1 | 74 |
| nonsense | 2 | 1 | 3 | |||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 4 | 6 | |||
| Total | 1 | 5 | 70 | 36 | 4 | 116 |
Highest pathogenic variant AF is 0.000012392234
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079202.2 | 18 | MANE Select | |
| Ensembl | ENSP00000419279.1 | 18 | MANE Select | |
| RefSeq | NP_001138392.1 | 17 | Standard | |
| RefSeq | NP_001138395.1 | 17 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ttc26 | Danio rerio | Structure: pronephric tubule Quality: distended abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Intraflagellar transport
- Cilium Assembly
- Organelle biogenesis and maintenance
Biological Process
- smoothened signaling pathway
- axoneme assembly
- intraciliary anterograde transport
- intraciliary transport involved in cilium assembly
- intraciliary transport
Molecular Function
- intraciliary transport particle B binding
Cellular Component
- centrosome
- cilium
- intraciliary transport particle B
- motile cilium
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000464848
- Coding exons
- 18
- Length
- 58243
- Individuals with no LoFs
- 125705
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 43
- Defined
- 125748
- p
- 0.000171
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.34 | 226 | 290 | 0.779 | 0.0000143 | 3675 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00027 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00043 | 0.00044 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.856
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.256
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |