NKX3-1
NK3 homeobox 1, the group of NKL subclass homeoboxes and pseudogenes
Basic information
Region (hg38): 8:23678696-23682938
Previous symbols: [ "NKX3A" ]
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 NKX3-1 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 | 2 | |||||
| missense | 16 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 1 | 2 |
Variants in NKX3-1
This is a list of pathogenic ClinVar variants found in the NKX3-1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-23681225-C-G | not specified | Uncertain significance (Sep 27, 2021) | ||
| 8-23681226-A-G | not specified | Uncertain significance (May 27, 2022) | ||
| 8-23681262-A-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 8-23681307-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 8-23681332-C-T | Benign (Jan 08, 2018) | |||
| 8-23681340-A-G | not specified | Uncertain significance (May 11, 2022) | ||
| 8-23681395-A-G | Benign (May 03, 2018) | |||
| 8-23681465-C-T | not specified | Uncertain significance (Jun 18, 2024) | ||
| 8-23681544-G-C | not specified | Uncertain significance (Feb 02, 2023) | ||
| 8-23681573-T-C | not specified | Uncertain significance (Jan 24, 2024) | ||
| 8-23681581-C-G | not specified | Likely benign (Aug 29, 2022) | ||
| 8-23682670-C-G | not specified | Uncertain significance (Dec 18, 2023) | ||
| 8-23682699-C-A | not specified | Uncertain significance (Oct 10, 2023) | ||
| 8-23682713-C-A | not specified | Uncertain significance (Aug 10, 2023) | ||
| 8-23682721-C-G | not specified | Uncertain significance (Jun 03, 2022) | ||
| 8-23682723-G-C | not specified | Uncertain significance (Mar 21, 2022) | ||
| 8-23682746-G-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 8-23682768-C-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 8-23682779-G-T | not specified | Uncertain significance (Mar 31, 2024) | ||
| 8-23682817-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 8-23682880-C-T | not specified | Uncertain significance (Feb 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NKX3-1 | protein_coding | protein_coding | ENST00000380871 | 2 | 4235 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000470 | 0.686 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.221 | 133 | 126 | 1.06 | 0.00000708 | 1461 |
| Missense in Polyphen | 56 | 49.111 | 1.1403 | 577 | ||
| Synonymous | 0.0249 | 60 | 60.2 | 0.996 | 0.00000350 | 489 |
| Loss of Function | 0.802 | 6 | 8.53 | 0.704 | 5.35e-7 | 96 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000600 | 0.0000600 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000548 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor, which binds preferentially the consensus sequence 5'-TAAGT[AG]-3' and can behave as a transcriptional repressor. Plays an important role in normal prostate development, regulating proliferation of glandular epithelium and in the formation of ducts in prostate. Acts as a tumor suppressor controlling prostate carcinogenesis, as shown by the ability to inhibit proliferation and invasion activities of PC-3 prostate cancer cells. {ECO:0000269|PubMed:19462257}.;
- Pathway
- Prostate cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Coregulation of Androgen receptor activity;FOXA1 transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.154
Haploinsufficiency Scores
- pHI
- 0.462
- hipred
- N
- hipred_score
- 0.461
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.500
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nkx3-1
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm;
Gene ontology
- Biological process
- metanephros development;somitogenesis;positive regulation of protein phosphorylation;regulation of transcription, DNA-templated;activation of cysteine-type endopeptidase activity involved in apoptotic process;multicellular organism development;salivary gland development;heart development;positive regulation of cell population proliferation;negative regulation of cell population proliferation;male gonad development;positive regulation of gene expression;negative regulation of gene expression;positive regulation of cell death;positive regulation of phosphatidylinositol 3-kinase signaling;cell differentiation;androgen receptor signaling pathway;regulation of protein localization;response to testosterone;cellular response to drug;dorsal aorta development;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;protein kinase B signaling;negative regulation of insulin-like growth factor receptor signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of mitotic cell cycle;positive regulation of mitotic cell cycle;positive regulation of transcription by RNA polymerase II;branching morphogenesis of an epithelial tube;negative regulation of epithelial cell proliferation;positive regulation of DNA-binding transcription factor activity;positive regulation of cell division;pharyngeal system development;branching involved in prostate gland morphogenesis;epithelial cell proliferation involved in salivary gland morphogenesis;negative regulation of epithelial cell proliferation involved in prostate gland development;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to steroid hormone stimulus;cellular response to hypoxia;mitotic cell cycle arrest;negative regulation of estrogen receptor binding;positive regulation of androgen secretion;positive regulation of response to DNA damage stimulus;positive regulation of apoptotic signaling pathway;positive regulation of intrinsic apoptotic signaling pathway
- Cellular component
- nucleus;site of DNA damage
- Molecular function
- transcription 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 factor activity;nuclear receptor activity;protein binding;transcription factor binding;cysteine-type endopeptidase activator activity involved in apoptotic process;estrogen receptor activity;estrogen receptor binding;histone deacetylase binding;sequence-specific DNA binding;protein self-association;transcription regulatory region DNA binding;MADS box domain binding