NKX6-1
NK6 homeobox 1, the group of NKL subclass homeoboxes and pseudogenes
Basic information
Region (hg38): 4:84491985-84499292
Previous symbols: [ "NKX6A" ]
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 NKX6-1 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 | 1 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 1 |
Variants in NKX6-1
This is a list of pathogenic ClinVar variants found in the NKX6-1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-84493303-C-G | not specified | Uncertain significance (Oct 04, 2024) | ||
| 4-84493426-C-T | not specified | Uncertain significance (Jun 18, 2021) | ||
| 4-84493449-C-G | not specified | Uncertain significance (Sep 02, 2024) | ||
| 4-84493490-C-T | Benign (Sep 21, 2018) | |||
| 4-84493491-G-T | not specified | Uncertain significance (Dec 09, 2023) | ||
| 4-84495703-T-C | not specified | Uncertain significance (Dec 31, 2024) | ||
| 4-84495801-G-C | not specified | Uncertain significance (Jan 17, 2025) | ||
| 4-84497666-C-G | not specified | Uncertain significance (Dec 04, 2024) | ||
| 4-84497750-A-G | not specified | Uncertain significance (Feb 07, 2023) | ||
| 4-84497823-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
| 4-84497832-C-G | not specified | Uncertain significance (Aug 21, 2024) | ||
| 4-84497873-G-A | not specified | Uncertain significance (Jan 19, 2025) | ||
| 4-84497880-A-G | not specified | Uncertain significance (Jan 20, 2025) | ||
| 4-84497904-C-G | not specified | Uncertain significance (Jul 12, 2023) | ||
| 4-84498068-G-A | not specified | Uncertain significance (Jan 17, 2023) | ||
| 4-84498084-A-G | not specified | Uncertain significance (Jul 10, 2024) | ||
| 4-84498092-C-G | not specified | Uncertain significance (Oct 17, 2024) | ||
| 4-84498161-G-T | not specified | Uncertain significance (Feb 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NKX6-1 | protein_coding | protein_coding | ENST00000295886 | 3 | 6464 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0627 | 0.876 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.08 | 90 | 124 | 0.728 | 0.00000588 | 2278 |
| Missense in Polyphen | 4 | 1.653 | 2.4198 | 40 | ||
| Synonymous | -0.411 | 60 | 56.1 | 1.07 | 0.00000294 | 812 |
| Loss of Function | 1.58 | 3 | 7.73 | 0.388 | 3.31e-7 | 121 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor which binds to specific A/T-rich DNA sequences in the promoter regions of a number of genes. Involved in the development of insulin-producing beta cells in the islets of Langerhans at the secondary transition (By similarity). Together with NKX2-2 and IRX3 acts to restrict the generation of motor neurons to the appropriate region of the neural tube. Belongs to the class II proteins of neuronal progenitor factors, which are induced by SHH signals (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:Q99MA9}.;
- Pathway
- Maturity onset diabetes of the young - Homo sapiens (human);Dopaminergic Neurogenesis;PTF1A related regulatory pathway
(Consensus)
Recessive Scores
- pRec
- 0.257
Haploinsufficiency Scores
- pHI
- 0.213
- hipred
- Y
- hipred_score
- 0.670
- ghis
- 0.546
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.575
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nkx6-1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- nkx6.1
- Affected structure
- secondary motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;neuron migration;transcription by RNA polymerase II;smoothened signaling pathway;animal organ morphogenesis;regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification;regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification;cell differentiation;regulation of axon extension;pancreas development;positive regulation of insulin secretion;response to nicotine;type B pancreatic cell proliferation;positive regulation of neuron differentiation;negative regulation of glial cell differentiation;positive regulation of glial cell differentiation;positive regulation of transcription by RNA polymerase II;oligodendrocyte differentiation;positive regulation of DNA-binding transcription factor activity;detection of glucose;cellular response to cytokine stimulus;cellular response to peptide hormone stimulus;type B pancreatic cell maturation;positive regulation of type B pancreatic cell development;regulation of neuron migration
- Cellular component
- nucleus;extracellular exosome
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;sequence-specific DNA binding