NKX1-2

NK1 homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:124445243-124450035

Previous symbols: [ "C10orf121" ]

Links

ENSG00000229544 ∙ NCBI:390010 ∙ ∙ HGNC:31652 ∙ Uniprot:Q9UD57 ∙ 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 NKX1-2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKX1-2 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						0
missense			39	3		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	3	0

Variants in NKX1-2

This is a list of pathogenic ClinVar variants found in the NKX1-2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-124447440-G-C		not specified	Uncertain significance (Jun 11, 2024)
10-124447442-G-T		not specified	Uncertain significance (Nov 13, 2023)
10-124447472-A-G		not specified	Uncertain significance (Dec 13, 2021)
10-124447514-G-C		not specified	Uncertain significance (Mar 08, 2025)
10-124447532-G-A		not specified	Uncertain significance (Dec 28, 2022)
10-124447553-G-A		not specified	Uncertain significance (Oct 30, 2023)
10-124447562-G-A		not specified	Uncertain significance (Oct 08, 2024)
10-124447586-C-G		not specified	Uncertain significance (Feb 26, 2025)
10-124447616-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-124447622-C-T		not specified	Uncertain significance (Apr 04, 2024)
10-124447641-C-A		not specified	Uncertain significance (Oct 03, 2022)
10-124447641-C-G		not specified	Likely benign (Apr 22, 2024)
10-124447668-C-T		not specified	Uncertain significance (Mar 27, 2023)
10-124447676-G-A		not specified	Uncertain significance (Nov 09, 2021)
10-124447686-C-T		not specified	Uncertain significance (Feb 20, 2025)
10-124447694-G-A		not specified	Uncertain significance (Jan 27, 2025)
10-124447717-C-G		not specified	Uncertain significance (Jun 17, 2024)
10-124447778-T-C		not specified	Uncertain significance (Mar 12, 2024)
10-124447785-G-A		not specified	Uncertain significance (Dec 20, 2022)
10-124447785-G-T		not specified	Uncertain significance (Apr 01, 2024)
10-124447850-G-A		not specified	Uncertain significance (Aug 21, 2023)
10-124447881-C-T		not specified	Uncertain significance (May 17, 2023)
10-124447886-T-C		not specified	Likely benign (Nov 17, 2023)
10-124447887-T-C		not specified	Uncertain significance (Sep 28, 2021)
10-124447934-G-A		not specified	Uncertain significance (Jan 02, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKX1-2	protein_coding	protein_coding	ENST00000451024	2	3162

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00278	0.588	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.225	100	93.9	1.07	0.00000438	1890
Missense in Polyphen		19	17.985	1.0564		456
Synonymous	-0.225	47	45.1	1.04	0.00000218	720
Loss of Function	0.367	4	4.87	0.821	2.14e-7	79

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in cell specification, particularly in the CNS. {ECO:0000250}.

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nkx1-2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding