PKNOX1

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

Basic information

Region (hg38): 21:42974510-43033931

Links

ENSG00000160199

∙ NCBI:5316 ∙ OMIM:602100 ∙ HGNC:9022 ∙ Uniprot:P55347 ∙ 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 PKNOX1 gene.

not_specified (34 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKNOX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004571.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			34 clinvar			34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKNOX1	protein_coding	protein_coding	ENST00000291547	10	59072

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00599	125675	0	70	125745	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	187	253	0.739	0.0000143	2865
Missense in Polyphen		51	97.938	0.52074		1135
Synonymous	-1.14	123	108	1.14	0.00000751	843
Loss of Function	4.17	2	24.0	0.0832	0.00000119	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000474	0.0000474
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000557	0.0000544
South Asian	0.00206	0.00206
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Activates transcription in the presence of PBX1A and HOXA1. {ECO:0000250|UniProtKB:O70477}.;
Pathway: Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

pRec: 0.141

Intolerance Scores

loftool
rvis_EVS: -0.47
rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

pHI: 0.177
hipred: Y
hipred_score: 0.654
ghis: 0.571

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pknox1
Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype; neoplasm; embryo phenotype; liver/biliary system phenotype; immune system phenotype;

Zebrafish Information Network

Gene name: pknox1.2
Affected structure: pharyngeal arch 3-7
Phenotype tag: abnormal
Phenotype quality: physical object quality

Gene ontology

Biological process: angiogenesis;transcription by RNA polymerase II;T cell differentiation;erythrocyte differentiation;camera-type eye development;positive regulation of transcription by RNA polymerase II
Cellular component: nucleus;transcription factor complex;cytoplasm
Molecular function: 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;protein heterodimerization activity