NKX2-3

NK2 homeobox 3, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:99532942-99536524

Previous symbols: [ "NKX2C" ]

Links

ENSG00000119919NCBI:159296OMIM:606727HGNC:7836Uniprot:Q8TAU0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NKX2-3 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
5
missense
39
clinvar
39
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 39 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NKX2-3protein_codingprotein_codingENST00000344586 23589
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9500.0494107038011070390.00000467
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8071371660.8240.000007432287
Missense in Polyphen5779.5080.716911137
Synonymous0.9046473.90.8660.00000348722
Loss of Function2.8509.460.004.01e-7129

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003170.0000317
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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