NKX2-3
Basic information
Region (hg38): 10:99532942-99536524
Previous symbols: [ "NKX2C" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKX2-3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145285.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 5 | |||||
missense | 39 | 39 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 39 | 5 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NKX2-3 | protein_coding | protein_coding | ENST00000344586 | 2 | 3589 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.950 | 0.0494 | 107038 | 0 | 1 | 107039 | 0.00000467 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.807 | 137 | 166 | 0.824 | 0.00000743 | 2287 |
Missense in Polyphen | 57 | 79.508 | 0.71691 | 1137 | ||
Synonymous | 0.904 | 64 | 73.9 | 0.866 | 0.00000348 | 722 |
Loss of Function | 2.85 | 0 | 9.46 | 0.00 | 4.01e-7 | 129 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000317 | 0.0000317 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
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 factor. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.202
Haploinsufficiency Scores
- pHI
- 0.740
- hipred
- Y
- hipred_score
- 0.669
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.983
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nkx2-3
- Phenotype
- immune system phenotype; skeleton phenotype; digestive/alimentary 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- leukocyte homeostasis;plasma cell differentiation;triglyceride metabolic process;biological_process;gland morphogenesis;cell differentiation;macrophage differentiation;regulation of cell population proliferation;odontogenesis of dentin-containing tooth;CD4-positive, alpha-beta T cell differentiation;positive regulation of transcription by RNA polymerase II;lymph node development;spleen development;Peyer's patch development;post-embryonic digestive tract morphogenesis;leukocyte migration
- Cellular component
- cellular_component;nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA-binding transcription factor activity;sequence-specific DNA binding