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Gene

CCDC40

coiled-coil domain 40 molecular ruler complex subunit

Summary

Cytogenetic location
17q25.3
Coordinates
Chromosome 17: 80,036,642–80,100,613 (GRCh38)
Exons
20 exons across 64 kb
Protein
1,142 amino acids
Inheritance
Autosomal recessive
Also known as
FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172, CFAP172
MANE Select transcript
ENST00000397545.9NM_017950.4
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

  • Primary Ciliary Dyskinesia

    • Autosomal recessive

      A rare, genetically heterogeneous, primarily respiratory disorder characterized by chronic upper and lower respiratory tract disease. Approximately half of PCD patients have an organ laterality defect (situs inversus totalis or situs ambiguus/heterotaxy).

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

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 CCDC40 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 17, with a bracket where CCDC40 sits. CCDC40 and 16 genes near it on chromosome 17, from 79,568,628 to 80,568,627.Chromosome 1717q25.3p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.379.6 Mb79.8 Mb80 Mb80.2 Mb80.4 MbRBFOX3: 79,089,345–79,611,317, reverse strandRBFOX3ENPP7: 79,728,809–79,742,930, forward strandENPP7CBX2: 79,778,135–79,788,394, forward strandCBX2CBX8: 79,792,132–79,801,683, reverse strandCBX8CBX4: 79,833,156–79,839,486, reverse strandCBX4TBC1D16: 79,932,343–80,035,887, reverse strandTBC1D16CCDC40: 80,036,642–80,100,613, forward strandCCDC40GAA: 80,101,526–80,119,881, forward strandGAAEIF4A3: 80,132,700–80,147,151, reverse strandEIF4A3CARD14: 80,169,992–80,216,073, forward strandCARD14SGSH: 80,206,716–80,220,928, reverse strandSGSHSLC26A11: 80,219,699–80,253,509, forward strandSLC26A11RNF213: 80,260,807–80,398,794, forward strandRNF213ENDOV: 80,415,147–80,438,086, forward strandENDOVNPTX1: 80,466,834–80,477,843, reverse strandNPTX1RPTOR: 80,544,819–80,966,371, forward strandRPTOR: 80,545,075–80,545,134, forward strandDiagram of CCDC40: 20 exons on the forward strand of chromosome 17Exon 2: 1 known disease-causing siteExon 3: 11 known disease-causing sitesExon 5: 6 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 7: 4 known disease-causing sitesExon 8: 5 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 10: 2 known disease-causing sitesExon 11: 6 known disease-causing sitesExon 12: 5 known disease-causing sitesExon 13: 3 known disease-causing sitesExon 14: 5 known disease-causing sitesExon 15: 5 known disease-causing sitesExon 16: 4 known disease-causing sitesExon 17: 3 known disease-causing sitesExon 18: 5 known disease-causing sitesExon 19: 7 known disease-causing sitesExon 20: 5 known disease-causing sitesExon 1: 80,036,642–80,036,691, 50 basesExon 2: 80,038,123–80,038,186, 64 basesExon 3: 80,039,812–80,040,270, 459 basesExon 4: 80,047,279–80,047,402, 124 basesExon 5: 80,048,583–80,048,761, 179 basesExon 6: 80,049,906–80,049,989, 84 basesExon 7: 80,050,064–80,050,283, 220 basesExon 8: 80,058,494–80,058,651, 158 basesExon 9: 80,058,858–80,058,980, 123 basesExon 10: 80,065,485–80,065,606, 122 basesExon 11: 80,081,546–80,081,789, 244 basesExon 12: 80,081,876–80,082,058, 183 basesExon 13: 80,084,743–80,084,988, 246 basesExon 14: 80,086,003–80,086,216, 214 basesExon 15: 80,087,607–80,087,776, 170 basesExon 16: 80,088,011–80,088,102, 92 basesExon 17: 80,089,764–80,089,884, 121 basesExon 18: 80,095,263–80,095,451, 189 basesExon 19: 80,097,245–80,097,403, 159 basesExon 20: 80,099,527–80,100,613, 1,087 bases124681012141618205′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 4.3 kb of the gene's 64 kb; 3,429 of those bases code for the protein.

How a genome test reads CCDC40

106

positions in CCDC40 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 64 kb of CCDC40, introns included, not only the 4.3 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.). CCDC40 gene: coiled-coil domain 40 molecular ruler complex subunit. Retrieved 16 October 2026, from https://dantelabs.com/genes/ccdc40

Vancouver

Dante Labs. CCDC40 gene: coiled-coil domain 40 molecular ruler complex subunit [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ccdc40

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