NKX2-8

NK2 homeobox 8, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 14:36580004-36582614

Previous symbols: [ "NKX2H" ]

Links

ENSG00000136327 ∙ NCBI:26257 ∙ OMIM:603245 ∙ HGNC:16364 ∙ Uniprot:O15522 ∙ 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 NKX2-8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKX2-8 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					2	2
missense			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	2

Variants in NKX2-8

This is a list of pathogenic ClinVar variants found in the NKX2-8 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-36580909-T-C		not specified	Uncertain significance (Aug 12, 2024)
14-36580910-T-C		not specified	Uncertain significance (May 27, 2022)
14-36580924-G-A		not specified	Uncertain significance (May 14, 2024)
14-36580925-C-T		not specified	Uncertain significance (Aug 16, 2022)
14-36580928-G-A		not specified	Uncertain significance (Feb 15, 2023)
14-36580948-G-A		not specified	Uncertain significance (Dec 01, 2022)
14-36580969-G-C		not specified	Uncertain significance (Aug 09, 2021)
14-36580984-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-36580988-G-T		not specified	Uncertain significance (Mar 10, 2025)
14-36580990-T-C		not specified	Uncertain significance (Jul 15, 2021)
14-36581008-G-A		not specified	Uncertain significance (Jun 24, 2022)
14-36581018-G-T		not specified	Uncertain significance (Mar 19, 2024)
14-36581030-A-G		not specified	Uncertain significance (Feb 28, 2024)
14-36581039-G-T		not specified	Uncertain significance (Feb 23, 2023)
14-36581041-G-T		not specified	Uncertain significance (Nov 29, 2021)
14-36581042-C-T		not specified	Uncertain significance (Nov 29, 2021)
14-36581079-G-C		not specified	Uncertain significance (Apr 12, 2024)
14-36581090-C-T		not specified	Uncertain significance (Jan 04, 2024)
14-36581122-C-T		not specified	Uncertain significance (Dec 03, 2021)
14-36581167-T-G		not specified	Uncertain significance (Dec 14, 2023)
14-36581176-T-C		not specified	Uncertain significance (Aug 17, 2022)
14-36581176-T-G		not specified	Uncertain significance (Jul 27, 2024)
14-36581192-C-T		not specified	Uncertain significance (Dec 03, 2024)
14-36581218-T-C		not specified	Uncertain significance (Dec 06, 2022)
14-36581239-A-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKX2-8	protein_coding	protein_coding	ENST00000258829	2	2029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00485	0.707	122493	0	10	122503	0.0000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.500	119	105	1.14	0.00000488	1453
Missense in Polyphen		35	34.352	1.0189		433
Synonymous	-1.75	66	50.2	1.32	0.00000246	537
Loss of Function	0.716	4	5.87	0.681	2.53e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000135	0.000132
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000620	0.0000561
Finnish	0.00	0.00
European (Non-Finnish)	0.0000295	0.0000272
Middle Eastern	0.0000620	0.0000561
South Asian	0.000101	0.0000991
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.374
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.145

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkx2-9
• Phenotype: cellular phenotype; neoplasm; 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); respiratory system phenotype

Gene ontology

• Biological process: liver development;transcription, DNA-templated;transcription by RNA polymerase II;axonogenesis;cell differentiation;lung development;positive regulation of transcription by RNA polymerase II;negative regulation of epithelial cell proliferation
• 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;DNA-binding transcription activator activity, RNA polymerase II-specific;double-stranded DNA binding;DNA-binding transcription factor activity;sequence-specific DNA binding