NKX6-3

NK6 homeobox 3, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 8:41645177-41650817

Links

ENSG00000165066 ∙ NCBI:157848 ∙ OMIM:610772 ∙ HGNC:26328 ∙ Uniprot:A6NJ46 ∙ 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 NKX6-3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKX6-3 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2		1	3
Total	0	0	13	0	1

Variants in NKX6-3

This is a list of pathogenic ClinVar variants found in the NKX6-3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-41646469-G-T		not specified	Uncertain significance (Jul 09, 2024)
8-41646492-C-A		not specified	Uncertain significance (Mar 19, 2024)
8-41646495-T-G		not specified	Uncertain significance (Oct 26, 2022)
8-41646501-C-A		not specified	Uncertain significance (Sep 06, 2022)
8-41646555-T-G		not specified	Uncertain significance (Dec 04, 2024)
8-41646585-C-G		not specified	Uncertain significance (Nov 23, 2021)
8-41646616-C-A		not specified	Uncertain significance (Aug 29, 2024)
8-41646619-G-T		not specified	Uncertain significance (Aug 22, 2023)
8-41646640-A-T		not specified	Uncertain significance (Jun 28, 2022)
8-41646660-T-C		not specified	Uncertain significance (Sep 26, 2024)
8-41646667-A-G		not specified	Uncertain significance (Apr 16, 2024)
8-41646701-T-A			Benign (Dec 26, 2018)
8-41647279-G-A		not specified	Uncertain significance (Dec 26, 2023)
8-41647283-C-A			Benign (Dec 26, 2018)
8-41647313-C-T		not specified	Uncertain significance (Apr 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKX6-3	protein_coding	protein_coding	ENST00000524115	2	6159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0165	0.723	124898	0	6	124904	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.112	75	72.3	1.04	0.00000351	829
Missense in Polyphen		28	21.365	1.3105		213
Synonymous	-0.103	36	35.2	1.02	0.00000201	290
Loss of Function	0.715	3	4.67	0.643	2.01e-7	54

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)	0.00000893	0.00000888
Middle Eastern	0.00	0.00
South Asian	0.000140	0.000131
Other	0.000176	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor, which may be involved in patterning of central nervous system and pancreas. {ECO:0000250}.

Intolerance Scores

• loftool: 0.206
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.16

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.361

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkx6-3
• Phenotype: digestive/alimentary phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: 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 activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding