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Gene

IFT54

intraflagellar transport 54

Summary

Cytogenetic location
2q37.3
Coordinates
Chromosome 2: 238,320,518–238,400,897 (GRCh38)
Exons
17 exons across 80.4 kb
Protein
691 amino acids
Inheritance
Autosomal recessive
Also known as
MIP-T3, DKFZP434F124, MIPT3, FAP116, CFAP116
Previous symbols
TRAF3IP1
MANE Select transcript
ENST00000373327.5NM_015650.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Nephronophthisis and Senior-Løken Syndrome

    • Senior-Løken SyndromeAutosomal recessive

      A form of nephronophthisis combined with retinal degeneration that can cause early vision loss.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing prompts referral for an eye examination alongside kidney monitoring.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How IFT54 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where IFT54 sits. IFT54 and 12 genes near it on chromosome 2, from 237,860,708 to 238,860,707.Chromosome 22q37.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3238 Mb238.2 Mb238.4 Mb238.6 Mb238.8 MbRAMP1: 237,858,893–237,923,438, forward strandRAMP1UBE2F: 237,966,827–238,051,730, forward strandUBE2FUBE2F-SCLY: 237,967,014–238,099,412, forward strandUBE2F-SCLYSCLY: 238,060,876–238,099,413, forward strandSCLYESPNL: 238,100,340–238,133,287, forward strandESPNLKLHL30: 238,138,649–238,152,947, forward strandKLHL30ERFE: 238,158,928–238,168,900, forward strandERFEILKAP: 238,170,399–238,203,761, reverse strandILKAPHES6: 238,237,903–238,240,680, reverse strandHES6PER2: 238,244,044–238,290,102, reverse strandPER2IFT54: 238,320,518–238,400,897, forward strandIFT54ASB1: 238,426,742–238,452,250, forward strandASB1TWIST2: 238,848,031–238,910,548, forward strandTWIST2Diagram of IFT54: 17 exons on the forward strand of chromosome 2Exon 5: 3 known disease-causing sitesExon 16: 1 known disease-causing siteExon 1: 238,320,518–238,320,785, 268 basesExon 2: 238,325,306–238,325,374, 69 basesExon 3: 238,325,809–238,325,970, 162 basesExon 4: 238,328,686–238,328,829, 144 basesExon 5: 238,328,926–238,329,342, 417 basesExon 6: 238,332,824–238,332,895, 72 basesExon 7: 238,333,960–238,334,035, 76 basesExon 8: 238,338,362–238,338,457, 96 basesExon 9: 238,344,497–238,344,598, 102 basesExon 10: 238,347,455–238,347,475, 21 basesExon 11: 238,348,764–238,348,848, 85 basesExon 12: 238,349,325–238,349,408, 84 basesExon 13: 238,352,827–238,352,950, 124 basesExon 14: 238,353,173–238,353,209, 37 basesExon 15: 238,356,004–238,356,080, 77 basesExon 16: 238,397,459–238,397,679, 221 basesExon 17: 238,398,754–238,400,897, 2,144 bases1246810121416175′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 4.2 kb of the gene's 80.4 kb; 2,076 of those bases code for the protein.

How a genome test reads IFT54

5

positions in IFT54 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 80.4 kb of IFT54, introns included, not only the 4.2 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). IFT54 gene: intraflagellar transport 54. Retrieved 16 October 2026, from https://dantelabs.com/genes/ift54

Vancouver

Dante Labs. IFT54 gene: intraflagellar transport 54 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ift54

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