Skip to content
Use your HSA or FSA funds
Sequence your genome (opens in a new tab)

Gene

CNOT1

CCR4-NOT transcription complex subunit 1

Summary

Cytogenetic location
16q21
Coordinates
Chromosome 16: 58,519,951–58,629,826 (GRCh38)
Exons
49 exons across 109.9 kb
Protein
2,376 amino acids
Also known as
CDC39, NOT1H, KIAA1007, AD-005
Previous symbols
NOT1
MANE Select transcript
ENST00000317147.10NM_016284.5
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Non-Acquired Combined Pituitary Hormone Deficiency

    • Congenital hypopituitarism is characterized by multiple pituitary hormone deficiency, including somatotroph, thyrotroph, lactotroph, corticotroph or gonadotroph deficiencies, due to mutations of pituitary transcription factors involved in pituitary ontogenesis.

      • 2 GenCC submitters rate it definitive or strong

How CNOT1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where CNOT1 sits. CNOT1 and 9 genes near it on chromosome 16, from 58,074,889 to 59,074,888.Chromosome 1616q21p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.358.2 Mb58.4 Mb58.6 Mb58.8 Mb59 MbCFAP20: 58,113,167–58,129,429, reverse strandCFAP20CSNK2A2: 58,157,907–58,198,191, reverse strandCSNK2A2CFAP263: 58,231,157–58,283,836, forward strandCFAP263PRSS54: 58,279,997–58,295,047, reverse strandPRSS54GINS3: 58,295,080–58,406,147, forward strandGINS3NDRG4: 58,462,846–58,513,628, forward strandNDRG4SETD6: 58,515,479–58,523,842, forward strandSETD6CNOT1: 58,519,951–58,629,826, reverse strandCNOT1SLC38A7: 58,663,015–58,684,770, reverse strandSLC38A7GOT2: 58,686,133–58,734,366, reverse strandGOT2Diagram of CNOT1: 49 exons on the reverse strand of chromosome 16Exon 48: 1 known disease-causing siteExon 43: 1 known disease-causing siteExon 28: 1 known disease-causing siteExon 23: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 20: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 7: 3 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 4: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 49: 58,519,951–58,521,036, 1,086 basesExon 48: 58,521,183–58,521,317, 135 basesExon 47: 58,523,370–58,523,502, 133 basesExon 46: 58,525,179–58,525,359, 181 basesExon 45: 58,525,989–58,526,138, 150 basesExon 44: 58,528,475–58,528,648, 174 basesExon 43: 58,530,246–58,530,347, 102 basesExon 42: 58,531,958–58,532,075, 118 basesExon 41: 58,532,232–58,532,395, 164 basesExon 40: 58,534,147–58,534,395, 249 basesExon 39: 58,536,989–58,537,220, 232 basesExon 38: 58,537,891–58,538,060, 170 basesExon 37: 58,538,158–58,538,266, 109 basesExon 36: 58,538,772–58,538,914, 143 basesExon 35: 58,539,768–58,539,959, 192 basesExon 34: 58,541,501–58,541,620, 120 basesExon 33: 58,542,231–58,542,335, 105 basesExon 32: 58,542,428–58,542,568, 141 basesExon 31: 58,543,607–58,543,903, 297 basesExon 30: 58,545,361–58,545,491, 131 basesExon 29: 58,546,321–58,546,498, 178 basesExon 28: 58,546,672–58,546,749, 78 basesExon 27: 58,547,186–58,547,296, 111 basesExon 26: 58,547,566–58,547,682, 117 basesExon 25: 58,549,719–58,549,898, 180 basesExon 24: 58,551,132–58,551,272, 141 basesExon 23: 58,551,589–58,551,819, 231 basesExon 22: 58,553,782–58,553,860, 79 basesExon 21: 58,555,251–58,555,537, 287 basesExon 20: 58,555,784–58,555,908, 125 basesExon 19: 58,556,847–58,556,993, 147 basesExon 18: 58,558,473–58,558,674, 202 basesExon 17: 58,560,212–58,560,362, 151 basesExon 16: 58,574,609–58,574,760, 152 basesExon 15: 58,575,007–58,575,129, 123 basesExon 14: 58,576,463–58,576,582, 120 basesExon 13: 58,578,699–58,578,939, 241 basesExon 12: 58,580,633–58,580,760, 128 basesExon 11: 58,581,345–58,581,515, 171 basesExon 10: 58,582,793–58,582,903, 111 basesExon 9: 58,583,056–58,583,182, 127 basesExon 8: 58,585,338–58,585,506, 169 basesExon 7: 58,586,545–58,586,748, 204 basesExon 6: 58,587,201–58,587,255, 55 basesExon 5: 58,587,345–58,587,413, 69 basesExon 4: 58,587,780–58,587,878, 99 basesExon 3: 58,588,799–58,588,906, 108 basesExon 2: 58,599,236–58,599,511, 276 basesExon 1: 58,629,728–58,629,826, 99 bases494540353025201510515′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 8.4 kb of the gene's 109.9 kb; 7,131 of those bases code for the protein.

Sequencing CNOT1

23

positions in CNOT1 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 109.9 kb of CNOT1, introns included, not only the 8.4 kb of exons.

ClinVar pathogenic variants (23)

The CNOT1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.

  • Pathogenic 10
  • Pathogenic/likely pathogenic 1
  • Likely pathogenic 12
VariantConditionsClinVar classificationReview status
NM_016284.5(CNOT1):c.1603C>T (p.Arg535Cys) (opens in a new tab)Vissers-Bodmer syndrome and 1 otherPathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
NM_016284.5(CNOT1):c.76C>T (p.Arg26Ter) (opens in a new tab)Vissers-Bodmer syndromePathogenic/likely pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
NM_016284.5(CNOT1):c.6959G>A (p.Trp2320Ter) (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.4800+1G>A (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.3055C>T (p.Gln1019Ter) (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.763_764del (p.Leu255fs) (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.445dup (p.Ile149fs) (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.434-2A>G (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.371_372dup (p.Gln125fs) (opens in a new tab)Vissers-Bodmer syndrome and 1 otherPathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.304C>T (p.Gln102Ter) (opens in a new tab)Vissers-Bodmer syndrome and 1 otherPathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.144dup (p.Arg49fs) (opens in a new tab)Vissers-Bodmer syndromePathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.6196delinsAA (p.Gln2066fs) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.3754_3756dup (p.Phe1252_Arg1253insPhe) (opens in a new tab)Vissers-Bodmer syndrome and 1 otherLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.3750+5G>A (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.3202-2dup (opens in a new tab)Vissers-Bodmer syndrome and 1 otherLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.2853T>G (p.Tyr951Ter) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.2560C>T (p.Arg854Ter) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.1004_1005dup (p.Trp336fs) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.920del (p.Gly307fs) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.550del (p.Leu184fs) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.439C>T (p.Gln147Ter) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.362T>G (p.Leu121Ter) (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter
NM_016284.5(CNOT1):c.102+2T>C (opens in a new tab)Vissers-Bodmer syndromeLikely pathogenic1 star out of 4 criteria provided, single submitter

Genes linked to the same conditions

Traits linked to CNOT1

The Human Phenotype Ontology lists these as features of the rare conditions CNOT1 can cause. Each trait's page lists the other genes linked to it.

External links

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 2026-10-18: 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 2026.10.18-8b139e39.

Cite this page

APA

Dante Labs. (n.d.). CNOT1 gene: CCR4-NOT transcription complex subunit 1. Retrieved 18 October 2026, from https://dantelabs.com/genes/cnot1

Vancouver

Dante Labs. CNOT1 gene: CCR4-NOT transcription complex subunit 1 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/cnot1

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test