IFT25
protein-codingintraflagellar transport 25, the group of Small heat shock proteins|IFT-B1 complex
Gene summary
Predicted to enable metal ion binding activity. Predicted to be involved in kidney development; smoothened signaling pathway; and spermatogenesis. Predicted to act upstream of or within several processes, including left/right axis specification; lung development; and skeletal system development. Part of intraciliary transport particle A. [provided by Alliance of Genome Resources, Jun 2026]
- C1orf41
- HSPB11
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.1 kbGenCC 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 IFT25 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016126.4. 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 | 0 | |||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 19 | 0 | 0 | 19 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057210.2 | 5 | MANE Select | |
| Ensembl | ENSP00000194214.5 | 5 | MANE Select | |
| RefSeq | NP_001303864.1 | 5 | Standard | |
| RefSeq | NP_001369178.1 | 4 | Standard |
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
- skeletal system development
- kidney development
- smoothened signaling pathway
- spermatogenesis
- heart development
Molecular Function
- protein binding
- metal ion binding
Cellular Component
- centrosome
- cilium
- intraciliary transport particle B
- ciliary tip
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000194214
- Coding exons
- 5
- Length
- 29356
- Individuals with no LoFs
- 124756
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 124772
- p
- 0.0000641
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.564 | 61 | 74.7 | 0.816 | 0.00000361 | 957 |
| Missense (PolyPhen) | 12 | 28.356 | 0.4232 | 383 | ||
| Synonymous | -0.656 | 32 | 27.6 | 1.16 | 0.00000164 | 253 |
| Loss of Function | 0.917 | 5 | 7.76 | 0.645 | 3.27e-7 | 95 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000093 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000090 | 0.000088 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly. Its role in intraflagellar transport is mainly seen in tissues rich in ciliated cells such as kidney and testis. Essential for male fertility, spermiogenesis and sperm flagella formation. Plays a role in the early development of the kidney. May be involved in the regulation of ureteric bud initiation (By similarity). {ECO:0000250|UniProtKB:Q9D6H2}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.476
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.33
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |