PKNOX1
PBX/knotted 1 homeobox 1, the group of TALE class homeoboxes and pseudogenes
Basic information
Region (hg38): 21:42974509-43033931
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in PKNOX1
This is a list of pathogenic ClinVar variants found in the PKNOX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-43004413-G-A | not specified | Uncertain significance (May 23, 2023) | ||
| 21-43010135-A-T | not specified | Uncertain significance (Feb 09, 2023) | ||
| 21-43010150-A-G | not specified | Uncertain significance (May 26, 2024) | ||
| 21-43010153-G-A | not specified | Uncertain significance (May 27, 2022) | ||
| 21-43013198-G-A | not specified | Uncertain significance (May 28, 2024) | ||
| 21-43016959-C-G | not specified | Uncertain significance (Dec 28, 2022) | ||
| 21-43016969-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 21-43018210-A-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 21-43021429-G-A | not specified | Uncertain significance (Apr 04, 2024) | ||
| 21-43028799-G-A | not specified | Uncertain significance (Jun 13, 2023) | ||
| 21-43028844-C-A | not specified | Uncertain significance (Mar 02, 2023) | ||
| 21-43028858-G-T | not specified | Uncertain significance (May 26, 2023) | ||
| 21-43029916-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 21-43029922-A-G | not specified | Uncertain significance (Sep 25, 2023) | ||
| 21-43030003-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 21-43030042-G-A | not specified | Uncertain significance (Apr 12, 2022) | ||
| 21-43030048-G-A | not specified | Uncertain significance (Mar 15, 2024) | ||
| 21-43030066-G-A | not specified | Uncertain significance (Jul 19, 2023) |
GnomAD
Source:
| 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:
- 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