NKX2-4

NK2 homeobox 4, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 20:21395365-21397526

Previous symbols: [ "NKX2D" ]

Links

ENSG00000125816 ∙ NCBI:644524 ∙ OMIM:607808 ∙ HGNC:7837 ∙ Uniprot:Q9H2Z4 ∙ 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 NKX2-4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKX2-4 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				1	1	2
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	1

Variants in NKX2-4

This is a list of pathogenic ClinVar variants found in the NKX2-4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-21395936-T-C		not specified	Uncertain significance (Oct 20, 2024)
20-21395966-C-A		not specified	Uncertain significance (Aug 12, 2021)
20-21396018-G-A		not specified	Uncertain significance (Mar 01, 2024)
20-21396059-G-C		not specified	Uncertain significance (Jun 23, 2023)
20-21396074-G-A		not specified	Uncertain significance (May 23, 2024)
20-21396092-G-A		not specified	Uncertain significance (Apr 04, 2024)
20-21396108-C-A		not specified	Uncertain significance (Jul 07, 2024)
20-21396125-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-21396141-C-T		not specified	Uncertain significance (Jan 30, 2025)
20-21396155-C-A		not specified	Uncertain significance (Apr 09, 2024)
20-21396173-G-A			Uncertain significance (Jan 22, 2024)
20-21396183-G-T		not specified	Uncertain significance (Jan 17, 2025)
20-21396198-C-T		not specified	Uncertain significance (May 06, 2024)
20-21396258-G-A		not specified	Uncertain significance (Mar 07, 2024)
20-21396274-C-G		not specified	Uncertain significance (Jun 03, 2024)
20-21396277-G-C			Benign (May 18, 2018)
20-21396299-A-C		not specified	Uncertain significance (Oct 17, 2023)
20-21396380-G-T		not specified	Uncertain significance (Jan 29, 2024)
20-21396384-G-C		not specified	Uncertain significance (Aug 28, 2024)
20-21396411-G-C		not specified	Uncertain significance (Dec 16, 2024)
20-21396413-G-A		not specified	Uncertain significance (Nov 15, 2024)
20-21396413-G-C		not specified	Uncertain significance (Dec 09, 2023)
20-21396431-G-A		not specified	Uncertain significance (May 20, 2024)
20-21396438-G-T		not specified	Uncertain significance (Aug 26, 2024)
20-21396443-G-C		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKX2-4	protein_coding	protein_coding	ENST00000351817	2	2662

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00448	0.690	122246	0	4	122250	0.0000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0799	115	113	1.02	0.00000528	2169
Missense in Polyphen		48	55.775	0.8606		871
Synonymous	-1.49	66	52.3	1.26	0.00000272	774
Loss of Function	0.666	4	5.72	0.699	2.46e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000117	0.000113
Finnish	0.00	0.00
European (Non-Finnish)	0.00000921	0.00000900
Middle Eastern	0.000117	0.000113
South Asian	0.0000337	0.0000335
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription factor.

Recessive Scores

• pRec: 0.139

Haploinsufficiency Scores

• pHI: 0.314
• hipred: Y
• hipred_score: 0.651
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.530

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkx2-4

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;biological_process;cell differentiation;positive regulation of transcription by RNA polymerase II
• 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