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Intellectual disability

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 4 panels

2 reviews

Louise Daugherty (Genomics England Curator)

Comment on phenotypes: added OMIM MIM id
Created: 19 Aug 2019, 9:40 a.m. | Last Modified: 19 Aug 2019, 9:40 a.m.
Panel Version: 2.1013

Rebecca Foulger (Genomics England curator)

Comment on list classification: Promoted to green on advice from Helen Brittain (Genomics England Clinical Fellow)- there are 3+ cases with a range of causative variants and a relevant phenotype.
Created: 18 Jun 2019, 2:32 p.m.
Comment on list classification: Added to panel as an Amber gene awaiting further evidence/clinical review. PMID:31006513 (De Franco et al., 2019) suggest the CNOT1 phenotype is variant-specific since the DDD project cases had developmental delay but no holoprosencephaly or pancreatic phenotypes. Developmental delay has been reported in the two holoprosencephaly cases from PMID:31006510 (Kruszka et al., 2019) but was not amongst the phenotypes reported in three holoprosencephaly patients from PMID:31006513 (despite carrying the same heterozygous p.Arg535Cys variant).
Created: 13 May 2019, 11:16 a.m.
Added CNOT1 to the ID panel based on recent (2019) literature evidence: 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]). Both probands had global developmental delay amongst their phenotypes.

De Franco et al., 2019 (PMID:31006513) report that the DDD study has identified de novo CNOT1 variants in three individuals with developmental delay (two missense variants p.Leu2323Phe and p.Arg623Trp, and and a nonsense variant p.Gln33*) not that none of them had holoprosencephaly or diabetes.
Sources: Literature
Created: 13 May 2019, 11:09 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
global developmental delay

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Holoprosencephaly 12, with or without pancreatic agenesis, 618500
  • global developmental delay
OMIM
604917
Clinvar variants
Variants in CNOT1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

19 Aug 2019, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: CNOT1 were changed from global developmental delay to Holoprosencephaly 12, with or without pancreatic agenesis, 618500; global developmental delay

18 Jun 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: cnot1 has been classified as 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: 1

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

Rebecca Foulger (Genomics England curator)

gene: CNOT1 was added gene: CNOT1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: CNOT1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CNOT1 were set to 31006510; 21679367; 31006513 Phenotypes for gene: CNOT1 were set to global developmental delay