NANOG
Nanog homeobox, the group of NKL subclass homeoboxes and pseudogenes
Basic information
Region (hg38): 12:7787794-7799146
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NANOG gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 2 | 0 |
Variants in NANOG
This is a list of pathogenic ClinVar variants found in the NANOG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-7789636-C-A | not specified | Uncertain significance (Oct 09, 2024) | ||
| 12-7789729-C-A | Likely benign (Jun 26, 2018) | |||
| 12-7792952-T-C | not specified | Uncertain significance (Oct 29, 2021) | ||
| 12-7792970-A-G | not specified | Uncertain significance (Jan 18, 2025) | ||
| 12-7793003-T-C | not specified | Uncertain significance (Feb 28, 2025) | ||
| 12-7793168-C-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 12-7793178-A-G | not specified | Uncertain significance (Sep 26, 2024) | ||
| 12-7794705-C-A | not specified | Uncertain significance (Jun 26, 2024) | ||
| 12-7794820-T-G | not specified | Uncertain significance (Aug 16, 2021) | ||
| 12-7794821-C-A | not specified | Uncertain significance (Aug 16, 2021) | ||
| 12-7794833-A-G | not specified | Uncertain significance (Dec 26, 2023) | ||
| 12-7794898-T-C | not specified | Uncertain significance (Nov 07, 2024) | ||
| 12-7795021-A-G | not specified | Uncertain significance (Mar 06, 2023) | ||
| 12-7795089-C-T | Likely benign (Dec 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NANOG | protein_coding | protein_coding | ENST00000229307 | 4 | 8266 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.720 | 0.277 | 124289 | 0 | 1 | 124290 | 0.00000402 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.400 | 128 | 141 | 0.905 | 0.00000655 | 2017 |
| Missense in Polyphen | 9 | 16.976 | 0.53015 | 309 | ||
| Synonymous | 0.796 | 45 | 52.3 | 0.860 | 0.00000273 | 520 |
| Loss of Function | 2.39 | 1 | 8.51 | 0.117 | 3.63e-7 | 98 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes. Acts as a transcriptional activator or repressor. Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'- [CG][GA][CG]C[GC]ATTAN[GC]-3'. Binds to the POU5F1/OCT4 promoter (PubMed:25825768). Able to autorepress its expression in differentiating (ES) cells: binds to its own promoter following interaction with ZNF281/ZFP281, leading to recruitment of the NuRD complex and subsequent repression of expression. When overexpressed, promotes cells to enter into S phase and proliferation. {ECO:0000269|PubMed:15983365, ECO:0000269|PubMed:16000880, ECO:0000269|PubMed:16391521, ECO:0000269|PubMed:25825768}.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Cardiac Progenitor Differentiation;Transcriptional regulation of pluripotent stem cells;Endoderm Differentiation;Mesodermal Commitment Pathway;Preimplantation Embryo;Wnt Signaling Pathway and Pluripotency;Interleukin-4 and 13 signaling;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Transcriptional regulation of pluripotent stem cells
(Consensus)
Recessive Scores
- pRec
- 0.342
Intolerance Scores
- loftool
- 0.200
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 68.98
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.485
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nanog
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- nanog
- Affected structure
- primordial germ cell
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised
Gene ontology
- Biological process
- endodermal cell fate specification;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;cell population proliferation;regulation of gene expression;cytokine-mediated signaling pathway;stem cell population maintenance;cell differentiation;somatic stem cell population maintenance;regulation of cell differentiation;positive regulation of transcription by RNA polymerase II;negative regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;nucleoplasm;nucleolus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding