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Gene

CEP290

centrosomal protein 290

Summary

Cytogenetic location
12q21.32
Coordinates
Chromosome 12: 88,049,016–88,142,088 (GRCh38)
Exons
54 exons across 93.1 kb
Protein
2,479 amino acids
Inheritance
Autosomal recessive
Also known as
KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3
MANE Select transcript
ENST00000552810.6NM_025114.4
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 reports relevant to this gene

  • Bardet-Biedl and Alström Syndromes

    • Bardet-Biedl syndromeAutosomal recessive

      A recessive ciliopathy caused by variants in more than 20 genes (most often BBS1 and BBS10) that causes retinal dystrophy, obesity, extra fingers or toes, kidney anomalies and learning difficulties.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Diagnosis allows eye, kidney and diabetes surveillance, and setmelanotide is an approved treatment for obesity in Bardet-Biedl syndrome.

  • Joubert Syndrome And Related Disorders

    • Autosomal recessive

      Joubert syndrome (JS) and related disorders (JSRD) are a group of developmental delay/multiple congenital anomaly syndromes in which the mandatory feature is the "molar tooth sign'' (MTS), a complex midbrain-hindbrain malformation recognizable on brain imaging. The MTS is characterized by cerebellar vermis hypodysplasia, thickening and malorientation of the superior cerebellar peduncles and abnormally deep interpeduncular fossa.

      • 2 GenCC submitters rate it definitive or strong
    • Joubert Syndrome

      A ciliopathy defined by a malformation of the cerebellum and brainstem (the molar tooth sign), with low muscle tone, developmental delay and abnormal eye movements, sometimes with kidney, liver or eye involvement.

      • 2 GenCC submitters rate it definitive or strong

  • Leber Congenital Amaurosis & RPE65-Related Retinopathy

    • Leber Congenital AmaurosisAutosomal recessive

      A group of inherited retinal dystrophies, caused by changes in genes such as CEP290, GUCY2D, CRB1, RPE65 and AIPL1, that cause severe vision loss, nystagmus and poor pupil responses in infancy.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Confirming the gene can determine eligibility for gene-specific treatments and clinical trials, and informs family counselling.

Broader groupings

  • Autosomal Recessive Cerebellar Ataxias (incl. CANVAS and AVED)

    • Autosomal Recessive Cerebellar AtaxiaAutosomal recessive

      One of 57 genes linked to it

      A group of recessively inherited ataxias caused by biallelic variants in genes such as RFC1, FXN, SACS, TTPA, SETX, APTX, PNKP, ANO10 and SYNE1.

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

      Ataxia with vitamin E deficiency (TTPA) is treatable with vitamin E supplements; other forms are managed with physiotherapy and symptom care, and relatives can be offered carrier testing.

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 CEP290 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 12, with a bracket where CEP290 sits. CEP290 and 4 genes near it on chromosome 12, from 87,595,552 to 88,595,551.Chromosome 1212q21.32p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.3387.6 Mb87.8 Mb88 Mb88.2 Mb88.4 MbZC3H11D: 87,980,035–88,034,037, reverse strandZC3H11DRLIG1: 88,033,846–88,050,160, forward strandRLIG1CEP290: 88,049,016–88,142,088, reverse strandCEP290TMTC3: 88,142,181–88,199,887, forward strandTMTC3KITLG: 88,492,789–88,580,851, reverse strandKITLGDiagram of CEP290: 54 exons on the reverse strand of chromosome 12Exon 54: 24 known disease-causing sitesExon 53: 8 known disease-causing sitesExon 52: 5 known disease-causing sitesExon 51: 10 known disease-causing sitesExon 50: 16 known disease-causing sitesExon 49: 15 known disease-causing sitesExon 48: 6 known disease-causing sitesExon 47: 20 known disease-causing sitesExon 46: 7 known disease-causing sitesExon 45: 13 known disease-causing sitesExon 44: 9 known disease-causing sitesExon 43: 16 known disease-causing sitesExon 42: 30 known disease-causing sitesExon 41: 12 known disease-causing sitesExon 40: 26 known disease-causing sitesExon 39: 13 known disease-causing sitesExon 38: 25 known disease-causing sitesExon 37: 31 known disease-causing sitesExon 36: 11 known disease-causing sitesExon 35: 25 known disease-causing sitesExon 34: 8 known disease-causing sitesExon 33: 11 known disease-causing sitesExon 32: 25 known disease-causing sitesExon 31: 49 known disease-causing sitesExon 30: 8 known disease-causing sitesExon 29: 11 known disease-causing sitesExon 28: 26 known disease-causing sitesExon 27: 9 known disease-causing sitesExon 26: 13 known disease-causing sitesExon 25: 21 known disease-causing sitesExon 24: 13 known disease-causing sitesExon 23: 10 known disease-causing sitesExon 22: 15 known disease-causing sitesExon 21: 13 known disease-causing sitesExon 20: 9 known disease-causing sitesExon 19: 10 known disease-causing sitesExon 18: 12 known disease-causing sitesExon 17: 12 known disease-causing sitesExon 16: 7 known disease-causing sitesExon 15: 19 known disease-causing sitesExon 14: 15 known disease-causing sitesExon 13: 10 known disease-causing sitesExon 12: 13 known disease-causing sitesExon 11: 4 known disease-causing sitesExon 10: 21 known disease-causing sitesExon 9: 21 known disease-causing sitesExon 8: 1 known disease-causing siteExon 7: 5 known disease-causing sitesExon 6: 21 known disease-causing sitesExon 5: 10 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 9 known disease-causing sitesExon 2: 11 known disease-causing sitesExon 54: 88,049,016–88,049,414, 399 basesExon 53: 88,050,354–88,050,433, 80 basesExon 52: 88,053,652–88,053,746, 95 basesExon 51: 88,054,340–88,054,413, 74 basesExon 50: 88,055,576–88,055,717, 142 basesExon 49: 88,058,848–88,059,020, 173 basesExon 48: 88,059,898–88,060,020, 123 basesExon 47: 88,060,830–88,060,994, 165 basesExon 46: 88,062,692–88,062,778, 87 basesExon 45: 88,063,981–88,064,115, 135 basesExon 44: 88,068,522–88,068,645, 124 basesExon 43: 88,071,294–88,071,449, 156 basesExon 42: 88,071,781–88,071,926, 146 basesExon 41: 88,077,222–88,077,344, 123 basesExon 40: 88,077,697–88,077,918, 222 basesExon 39: 88,079,092–88,079,229, 138 basesExon 38: 88,080,182–88,080,395, 214 basesExon 37: 88,083,031–88,083,230, 200 basesExon 36: 88,083,847–88,083,954, 108 basesExon 35: 88,084,586–88,084,852, 267 basesExon 34: 88,086,039–88,086,173, 135 basesExon 33: 88,086,391–88,086,498, 108 basesExon 32: 88,087,780–88,087,944, 165 basesExon 31: 88,089,032–88,089,487, 456 basesExon 30: 88,090,728–88,090,839, 112 basesExon 29: 88,092,681–88,092,832, 152 basesExon 28: 88,093,770–88,093,975, 206 basesExon 27: 88,096,888–88,096,999, 112 basesExon 26: 88,102,838–88,103,011, 174 basesExon 25: 88,106,675–88,106,905, 231 basesExon 24: 88,106,996–88,107,098, 103 basesExon 23: 88,109,066–88,109,181, 116 basesExon 22: 88,111,202–88,111,351, 150 basesExon 21: 88,111,694–88,111,858, 165 basesExon 20: 88,114,420–88,114,562, 143 basesExon 19: 88,115,098–88,115,182, 85 basesExon 18: 88,117,033–88,117,145, 113 basesExon 17: 88,118,483–88,118,570, 88 basesExon 16: 88,118,643–88,118,743, 101 basesExon 15: 88,120,114–88,120,276, 163 basesExon 14: 88,120,997–88,121,166, 170 basesExon 13: 88,125,246–88,125,369, 124 basesExon 12: 88,126,316–88,126,438, 123 basesExon 11: 88,128,946–88,129,035, 90 basesExon 10: 88,129,694–88,129,876, 183 basesExon 9: 88,130,268–88,130,420, 153 basesExon 8: 88,130,545–88,130,565, 21 basesExon 7: 88,131,165–88,131,218, 54 basesExon 6: 88,136,643–88,136,786, 144 basesExon 5: 88,139,145–88,139,191, 47 basesExon 4: 88,139,495–88,139,564, 70 basesExon 3: 88,140,956–88,141,033, 78 basesExon 2: 88,141,206–88,141,334, 129 basesExon 1: 88,141,900–88,142,088, 189 bases54504540353025201510515′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 7.8 kb of the gene's 93.1 kb; 7,440 of those bases code for the protein.

How a genome test reads CEP290

906

positions in CEP290 where ClinVar classes a change as pathogenic or likely pathogenic

24 of them (2.6%) fall in regions short reads find hard.

  • Segmental duplications (24 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 93.1 kb of CEP290, introns included, not only the 7.8 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.). CEP290 gene: centrosomal protein 290. Retrieved 17 October 2026, from https://dantelabs.com/genes/cep290

Vancouver

Dante Labs. CEP290 gene: centrosomal protein 290 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cep290

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