CNOT7

Chr 8

CCR4-NOT transcription complex subunit 7

Also known as: CAF-1, CAF1, Caf1a, hCAF-1

NCBI Gene: 29883ENSG00000198791UniProt: Q9UIV1

The CNOT7 protein is a catalytic component of the CCR4-NOT complex that functions as a 3'-5' poly(A) exoribonuclease, playing a central role in mRNA deadenylation, degradation, and translational regulation. Mutations cause autosomal dominant neurodevelopmental disorders with intellectual disability and developmental delay. This gene is highly constrained against loss-of-function variants (pLI = 0.997), indicating that haploinsufficiency is likely not tolerated in the general population.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
8
Pubs (1 yr)
80
P/LP submissions
0%
P/LP missense
0.18
LOEUF· LoF intol.
—
Mechanism
Clinical Summary— CNOT7
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
80 unique Pathogenic / Likely Pathogenic· 24 VUS of 120 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.18LOEUF
pLI 0.997
Z-score 3.82
OE 0.00 (0.00–0.18)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.63Z-score
OE missense 0.40 (0.33–0.50)
61 obs / 152.3 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.00 (0.00–0.18)
0≤0.351.4
Missense OE0.40 (0.33–0.50)
0≤0.61.4
Synonymous OE1.24
0≤1.21.6
LoF obs/exp: 0 / 17.0Missense obs/exp: 61 / 152.3Syn Z: -1.36

ClinVar Variant Classifications

120 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic76
Likely Pathogenic4
VUS24
Likely Benign2
Benign1
76
Pathogenic
4
Likely Pathogenic
24
VUS
2
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
76
0
76
Likely Pathogenic
0
0
4
0
4
VUS
0
15
9
0
24
Likely Benign
0
0
1
1
2
Benign
0
0
1
0
1
Total015911107

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CNOT7 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients