NKX2-3

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

Basic information

Region (hg38): 10:99532941-99536524

Previous symbols: [ "NKX2C" ]

Links

ENSG00000119919 ∙ NCBI:159296 ∙ OMIM:606727 ∙ HGNC:7836 ∙ Uniprot:Q8TAU0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

• Inborn genetic diseases (13 variants)
• not provided (3 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.

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				3		3
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	3	0

Variants in NKX2-3

This is a list of pathogenic ClinVar variants found in the NKX2-3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-99533202-A-G		not specified	Uncertain significance (Feb 26, 2024)
10-99533268-T-C		not specified	Uncertain significance (Apr 07, 2022)
10-99533282-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-99533286-G-A		not specified	Uncertain significance (Oct 27, 2023)
10-99533331-G-C		not specified	Uncertain significance (Sep 25, 2023)
10-99533384-T-G		not specified	Uncertain significance (Sep 29, 2022)
10-99533428-C-G		not specified	Uncertain significance (May 13, 2022)
10-99533438-G-A		not specified	Uncertain significance (Aug 11, 2022)
10-99533451-A-G		not specified	Uncertain significance (Dec 22, 2023)
10-99533462-C-A		not specified	Uncertain significance (Aug 02, 2021)
10-99533477-G-T		not specified	Uncertain significance (Jan 07, 2022)
10-99535078-C-T		not specified	Uncertain significance (Nov 09, 2023)
10-99535094-G-A			Likely benign (Jul 01, 2022)
10-99535128-A-G		not specified	Uncertain significance (Dec 13, 2022)
10-99535240-G-A		not specified	Uncertain significance (Apr 07, 2023)
10-99535305-G-A		not specified	Uncertain significance (Jun 21, 2023)
10-99535329-G-C		not specified	Uncertain significance (Apr 28, 2023)
10-99535368-G-A		not specified	Uncertain significance (Feb 15, 2024)
10-99535413-C-T		not specified	Uncertain significance (Dec 21, 2021)
10-99535472-A-T			Likely benign (Sep 01, 2022)
10-99535475-A-T			Likely benign (Sep 01, 2022)
10-99535488-A-G		not specified	Uncertain significance (Nov 10, 2022)
10-99535546-C-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

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: 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

	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