NKX6-2 NK6 homeobox 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NKX6-2provided by HGNC
Official Full Name: NK6 homeobox 2provided by HGNC
Primary source: HGNC:HGNC:19321
See related: Ensembl:ENSG00000148826 MIM:605955; AllianceGenome:HGNC:19321
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GTX; NKX6B; SPAX8; NKX6.2
Summary: Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; regulation of myelination; and regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including negative regulation of transcription by RNA polymerase II; neurogenesis; and neuromuscular process controlling balance. Predicted to be part of chromatin. Predicted to be active in nucleus. Implicated in spastic ataxia 8. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in stomach (RPKM 17.5), brain (RPKM 14.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q26.3

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (132783181..132786147, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (133732363..133735334, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (134596685..134599651, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

One-step Reprogramming of Human Fibroblasts into Oligodendrocyte-like Cells by SOX10, OLIG2, and NKX6.2.
Title: One-step Reprogramming of Human Fibroblasts into Oligodendrocyte-like Cells by SOX10, OLIG2, and NKX6.2.
A homozygous missense variant in the homeobox domain of the NKX6-2 results in progressive spastic ataxia type 8 associated with lower limb weakness and neurological manifestations.
Title: A homozygous missense variant in the homeobox domain of the NKX6-2 results in progressive spastic ataxia type 8 associated with lower limb weakness and neurological manifestations.
NK6 Homeobox 2 Regulated Gastrokin-2 Suppresses Gastric Cancer Cell Proliferation and Invasion via Akt Signaling Pathway.
Title: NK6 Homeobox 2 Regulated Gastrokin-2 Suppresses Gastric Cancer Cell Proliferation and Invasion via Akt Signaling Pathway.
Genetic and phenotypic characterization of NKX6-2-related spastic ataxia and hypomyelination.
Title: Genetic and phenotypic characterization of NKX6-2-related spastic ataxia and hypomyelination.
Expanding the clinical and neuroimaging features of NKX6-2-related hereditary spastic ataxia type 8.
Title: Expanding the clinical and neuroimaging features of NKX6-2-related hereditary spastic ataxia type 8.
Using whole-exome or whole-genome sequencing, we identified the previously reported c.196delC and c.487C>G variants in NKX6-2 in 3 and 2 unrelated index cases, respectively; the novel c.608G>A variant was identified in a sixth patient. All variants were homozygous in affected family members only.
Title: Expanding the clinical and genetic spectra of NKX6-2-related disorder.
This study showed that the finding of individuals with a severe neurodevelopemental phenotype with hypomyelination associated with biallelic mutations in NKX6-2 provides direct evidence of the relevant role of NKX6-2 in CNS development in humans.
Title: Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy.
NKX6-2 mutations should be considered in the differential diagnosis of spastic ataxia and hypomyelination.
Title: Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy MedGen: C4479653 OMIM: 617560 GeneReviews: NKX6-2-Related Disorder	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:486958

RH104158 (e-PCR)
- UniSTS:98483

Homology

Homologs of the NKX6-2 gene: The NKX6-2 gene is conserved in chimpanzee, Rhesus monkey, dog, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 458 organisms have orthologs with human gene NKX6-2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in central nervous system myelination	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell fate commitment	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
involved_in neuron fate commitment	IEA Inferred from Electronic Annotation more info
involved_in pancreatic A cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell fate commitment	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of myelination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: homeobox protein Nkx-6.2

Names: NK homeobox family 6, B; NK6 transcription factor related, locus 2; glial and testis-specific homeobox protein; homeobox 6B; homeobox protein NK-6 homolog B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_177400.3 → NP_796374.2 homeobox protein Nkx-6.2

Status: VALIDATED

Source sequence(s)

AL392043

Consensus CDS

CCDS7670.1

UniProtKB/Swiss-Prot

Q5JSF3

Related

ENSP00000357581.5, ENST00000368592.8

Conserved Domains (1) summary

pfam00046
Location:151 → 204

Homeobox; Homeobox domain