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Fetal anomalies

Gene: CNOT1

Green List (high evidence)

CNOT1 (CCR4-NOT transcription complex subunit 1)
EnsemblGeneIds (GRCh38): ENSG00000125107
EnsemblGeneIds (GRCh37): ENSG00000125107
OMIM: 604917, Gene2Phenotype
CNOT1 is in 5 panels

1 review

Rebecca Foulger (Genomics England curator)

Green List (high evidence)

Upgraded from Amber to Green following advice from Anna de Burca (Genomics England clinical team) and a Fetal Working Group call on July 19th 2019. Phenotypes are relevant to this panel (holoprosencephaly and pancreatic agenesis), sufficient cases (4/5), although phenotype may be variant-specific.
Created: 25 Jul 2019, 8:04 a.m. | Last Modified: 25 Jul 2019, 8:04 a.m.
Panel Version: 0.311
Keep as amber and added watchlist tag on advice from Helen Brittain (Genomics England Clinical Fellow);this might be a specific variant-related phenotype, and there is insufficient evidence for the gene in general at present.
Created: 18 Jun 2019, 2:30 p.m.
Comment on list classification: Kept rating as Amber awaiting clinical review. In summary: Probable rating in DDG2P. Sufficient (five) unrelated cases from two 2019 papers (PMID:31006513 and PMID:31006510) with holoprosencephaly, and pancreatic agenesis in 4/5 cases. The same heterozygous variant was recorded in all five individuals and authors of PMID:31006513 suggest phenotype is variant-specific rather than LOF. Mice require a homozygous variant to display a phenotype.
Created: 13 May 2019, 9:31 a.m.
Kruszka et al., 2019 (PMID:31006510) report two unrelated individuals with semilobar holoprosencephaly who have the identical de novo missense variant in the gene CNOT1. (c.1603C>T [p.Arg535Cys]). Proband 1 was born after a pregnancy complicated by IUGR. Additional medical problems include diabetes, pancreatice exocrine insufficiency and facial characteristics. No diabetic or pancreatic phenotype was recorded for proband 2.
Created: 13 May 2019, 9:28 a.m.
De Franco et al., 2019 (PMID:31006513) investigated a cohort of 107 individuals with pancreatic agenesis and definite/possible holoprosencephaly, and identified a heterozygous missense variant in CNOT1 (NM_016284.4; c.1603C>T (p.Arg535Cys)) in three unrelated individuals. The variant was de novo in two individuals, and was not present in the DNA sample from the third individual's father (maternal sample was unavailable). Mice required a homozygous variant to display a phenotype: in homozygous mice embryos (embryonically lethal) morphological abnormalities were apparent upon dissection including edema, a smaller dorsal pancreas, and exencephaly. The DDD study identified de novo CNOT1 variants in three individuals with developmental delay but none had holoprosencephaly, diabetes or pancreatic or neurological structural malformations. The authors therefore suggest that a mutation-specific mechanism rather than LOF is responsible for the pancreatic and holoprosencephaly phenotype.
Created: 13 May 2019, 9:27 a.m.
New gene:disorder association added to DDG2P on 25/04/2019: pancreatic agenesis and holoprosencephaly syndrome. Disease confidence rating in DDG2P: probable. DDG2P mutation consequence: all missense/in frame. DDG2P mode of inheritance: monoallelic.
Created: 13 May 2019, 9:25 a.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
Phenotypes
  • Holoprosencephaly 12, with or without pancreatic agenesis, 618500
OMIM
604917
Clinvar variants
Variants in CNOT1
Penetrance
None
Publications
Mode of Pathogenicity
Other - please provide details in the comments
Panels with this gene

History Filter Activity

12 Dec 2019, Gel status: 3

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: CNOT1 were changed from pancreatic agenesis and holoprosencephaly syndrome to Holoprosencephaly 12, with or without pancreatic agenesis, 618500

25 Jul 2019, Gel status: 3

Added New Source, Status Update

Rebecca Foulger (Genomics England curator)

Source Expert Review Green was added to CNOT1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

13 May 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: cnot1 has been classified as Amber List (Moderate Evidence).

13 May 2019, Gel status: 2

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set mode of pathogenicity

Rebecca Foulger (Genomics England curator)

gene: CNOT1 was added gene: CNOT1 was added to Fetal anomalies. Sources: DD-Gene2Phenotype,Expert Review Amber Mode of inheritance for gene: CNOT1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CNOT1 were set to 31006510; 31006513 Phenotypes for gene: CNOT1 were set to pancreatic agenesis and holoprosencephaly syndrome Mode of pathogenicity for gene: CNOT1 was set to Other - please provide details in the comments