PKNOX2

PBX/knotted 1 homeobox 2, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 11:125164686-125433389

Links

ENSG00000165495 ∙ NCBI:63876 ∙ OMIM:613066 ∙ HGNC:16714 ∙ Uniprot:Q96KN3 ∙ 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 PKNOX2 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKNOX2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in PKNOX2

This is a list of pathogenic ClinVar variants found in the PKNOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-125367879-C-G		not specified	Uncertain significance (Jul 13, 2021)
11-125367925-T-C		not specified	Uncertain significance (Dec 14, 2021)
11-125367939-A-C		not specified	Uncertain significance (Sep 01, 2021)
11-125367964-C-A		not specified	Uncertain significance (Nov 22, 2023)
11-125367973-G-A		not specified	Uncertain significance (May 17, 2023)
11-125385655-A-C		not specified	Uncertain significance (Apr 12, 2022)
11-125385715-A-G		not specified	Uncertain significance (Jul 13, 2022)
11-125398009-G-T		not specified	Uncertain significance (Jan 23, 2024)
11-125410275-T-A		not specified	Uncertain significance (Mar 22, 2023)
11-125410304-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-125410787-T-G		not specified	Uncertain significance (Jun 02, 2023)
11-125410850-G-A		not specified	Uncertain significance (Jun 01, 2023)
11-125411833-A-C		not specified	Uncertain significance (Jun 26, 2023)
11-125430117-G-A		not specified	Uncertain significance (Oct 18, 2021)
11-125431166-G-T		not specified	Uncertain significance (Dec 16, 2022)
11-125431171-A-G		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
11-125431180-G-A		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKNOX2	protein_coding	protein_coding	ENST00000298282	10	268703

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00826	124793	0	5	124798	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	198	274	0.722	0.0000148	3112
Missense in Polyphen		29	81.777	0.35463		938
Synonymous	-1.28	138	120	1.15	0.00000748	920
Loss of Function	4.08	2	23.2	0.0863	0.00000107	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000558	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.0732
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.600
• hipred: Y
• hipred_score: 0.699
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pknox2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasm;actin cytoskeleton;microtubule cytoskeleton;intercellular bridge
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;actin monomer binding;actin filament binding