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GeneE
6 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
IFT54
intraflagellar transport 54
Chromosome 2 Β· 2q37.3
NCBI Gene: 26146Ensembl: ENSG00000204104.13HGNC: HGNC:17861UniProt: Q8TDR0
41PubMed Papers
21Diseases
0Drugs
41Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Swiss-Prot Reviewed
Senior-Loken syndrome 9Senior-Loken syndromeneurodegenerative diseaseJeune syndrome
✦AI Summary

IFT54 is a component of the intraflagellar transport (IFT) complex B involved in bidirectional trafficking within cilia 1. During anterograde movement, IFT54 binds active kinesin-II along the ciliary microtubule axoneme while transporting the inactive dynein-2 complex for retrograde movement 1. IFT54 contains a divergent N-terminal Calponin Homology domain important for its molecular function 1. Beyond canonical ciliogenesis, IFT54 functions as a negative regulator of microtubule stability through MAP4 control, contributing to epithelial polarity in non-ciliary contexts 2. IFT54 is essential for immune synapse assembly, where it functions within an IFT20 complex regulating TCR recycling and phosphotyrosine signaling at the immune synapse 3. During cardiogenesis, IFT54 modulates the Hippo pathway effector YAP1, restricting proepicardium and myocardium formation 4. SMYD3-mediated regulation of IFT54 trafficking is critical for cilia formation and maintenance 5. Clinically, mutations in IFT54 cause Senior-Loken syndrome, a ciliopathy characterized by nephronophthisis and retinal degeneration 2. IFT54's transition fiber protein interactions are required for ciliary entry of assembled IFT particles 6.

Sources cited
1
IFT54 is a component of IFT-B complex; binds kinesin-II during anterograde movement and carries inactive dynein-2; contains NN-CH domain
PMID: 38551798
2
IFT54/TRAF3IP1 mutations cause nephronophthisis; IFT54 negatively regulates microtubule stability via MAP4 control
PMID: 26487268
3
IFT54 interacts with IFT20 complex; required for TCR accumulation and phosphotyrosine signaling at immune synapse
PMID: 28154159
4
IFT54 modulates Hippo pathway effector YAP1 during cardiogenesis to restrict proepicardium and myocardium formation
PMID: 32698004
5
SMYD3 regulates IFT54 trafficking; IFT54 trafficking is important for cilia formation and maintenance
PMID: 38892227
6
IFT54 interacts with transition fiber protein FBF1; required for ciliary entry of assembled IFT particles
PMID: 24231678
Disease Associationsβ“˜21
Senior-Loken syndrome 9Open Targets
0.72Strong
Senior-Loken syndromeOpen Targets
0.68Moderate
neurodegenerative diseaseOpen Targets
0.52Moderate
Jeune syndromeOpen Targets
0.42Moderate
short-rib thoracic dysplasia 6 with or without polydactylyOpen Targets
0.42Moderate
ciliopathyOpen Targets
0.37Weak
short rib-polydactyly syndrome, Majewski typeOpen Targets
0.37Weak
response to xenobiotic stimulusOpen Targets
0.33Weak
poisoningOpen Targets
0.32Weak
insomniaOpen Targets
0.32Weak
Progressive visual lossOpen Targets
0.31Weak
ovarian dysfunctionOpen Targets
0.28Weak
glaucomaOpen Targets
0.22Weak
genetic disorderOpen Targets
0.19Weak
Ellis Van Creveld syndromeOpen Targets
0.12Weak
Ellis-van Creveld syndromeOpen Targets
0.12Weak
Fuchs endothelial corneal dystrophyOpen Targets
0.08Suggestive
congenital hereditary endothelial dystrophy of corneaOpen Targets
0.07Suggestive
keratoconus 5Open Targets
0.07Suggestive
Lisch epithelial corneal dystrophyOpen Targets
0.07Suggestive
Senior-Loken syndrome 9UniProt
Pathogenic Variants41
NC_000002.12:g.238332824_238332827delPathogenic
not provided|Senior-Loken syndrome 9
β˜…β˜…β˜†β˜†2025
NM_015650.4(TRAF3IP1):c.551_554del (p.Gln184fs)Pathogenic
Senior-Loken syndrome 9|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 184
NM_015650.4(IFT54):c.988-1G>CLikely pathogenic
Short-rib thoracic dysplasia 6 with or without polydactyly|not provided|TRAF3IP1-related disorder
β˜…β˜…β˜†β˜†2024
NM_015650.4(TRAF3IP1):c.1388_1395dup (p.Pro466fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 466
NM_015650.4(TRAF3IP1):c.1159+1G>CLikely pathogenic
not provided|Cervical cancer
β˜…β˜†β˜†β˜†2025
NM_015650.4(TRAF3IP1):c.916-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_015650.4(TRAF3IP1):c.1716G>A (p.Trp572Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 572
NM_015650.4(TRAF3IP1):c.657_658dup (p.Ala220fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 220
NM_015650.4(TRAF3IP1):c.988-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_015650.4(TRAF3IP1):c.1693C>T (p.Arg565Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 565
NM_015650.4(TRAF3IP1):c.345del (p.Leu116fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 116
NM_015650.4(TRAF3IP1):c.761dup (p.Lys257fs)Likely pathogenic
Senior-Loken syndrome 9
β˜…β˜†β˜†β˜†2024β†’ Residue 257
NM_015650.4(TRAF3IP1):c.774_775del (p.Lys259fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 259
NM_015650.4(TRAF3IP1):c.802G>T (p.Glu268Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 268
NM_015650.4(TRAF3IP1):c.799C>T (p.Arg267Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 267
NM_015650.4(TRAF3IP1):c.915+1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_015650.4(TRAF3IP1):c.771del (p.Glu258fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 258
NM_015650.4(TRAF3IP1):c.1159G>T (p.Gly387Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 387
NM_015650.4(TRAF3IP1):c.796del (p.Asp266fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 266
NM_015650.4(TRAF3IP1):c.702_703del (p.Gly235fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 235
View on ClinVar β†—
Related Genes
IFT27Protein interaction100%IFT46Protein interaction100%IFT22Protein interaction100%IFT52Protein interaction100%IFT81Protein interaction100%IFT74Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Heart
86%
Ovary
85%
Liver
71%
Lung
63%
Bone Marrow
40%
Gene Interaction Network
Click a node to explore
IFT54IFT27IFT46IFT22IFT52IFT81IFT74
PROTEIN STRUCTURE
Preparing viewer…
PDB2EQO Β· NMR
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.72LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.57 [0.45–0.72]
RankingsWhere IFT54 stands among ~20K protein-coding genes
  • #10,020of 20,598
    Most Researched41
  • #1,522of 5,498
    Most Pathogenic Variants41
  • #5,594of 17,882
    Most Constrained (LOEUF)0.72
Genes detectedIFT54
Sources retrieved6 papers
Response timeβ€”
πŸ“„ Sources
6β–Ό
1
Intraflagellar Transport Complex B Proteins Regulate the Hippo Effector Yap1 during Cardiogenesis.
PMID: 32698004
Cell Rep Β· 2020
1.00
2
The T cell IFT20 interactome reveals new players in immune synapse assembly.
PMID: 28154159
J Cell Sci Β· 2017
0.83
3
PMID: 38551798
Biomol NMR Assign Β· 2024
0.67
4
SMYD3 Controls Ciliogenesis by Regulating Distinct Centrosomal Proteins and Intraflagellar Transport Trafficking.
PMID: 38892227
Int J Mol Sci Β· 2024
0.50
5
Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization.
PMID: 26487268
Nat Commun Β· 2015
0.33