NANOG
Chr 12Nanog homeobox
NANOG encodes a homeobox transcription factor that maintains embryonic stem cell pluripotency and prevents cellular differentiation by binding to specific DNA sequences and regulating target gene expression. Mutations cause autosomal dominant intellectual disability with distinctive facial features and variable developmental anomalies. The gene has an associated GeneReviews entry, indicating established clinical significance in human disease.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
95 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 41 | 0 | 41 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 31 | 9 | 0 | 40 |
Likely Benign | 0 | 0 | 1 | 1 | 2 |
Benign | 0 | 0 | 3 | 0 | 3 |
Conflicting | — | 1 | |||
| Total | 0 | 31 | 56 | 1 | 89 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NANOG · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Spermatogonial Differentiation Via Testicular Organoid
RECRUITINGEndoscopic Injection of Autologous, Activated and Emulsified Fat in Chronic Fistulas of the Gastrointestinal Tract and Pelvic Organs
RECRUITINGRole of BMP Pathway in MDS Progression
NOT YET RECRUITINGExternal Resources
Links to major genomics databases and tools