PNKD
Basic information
Region (hg38): 2:218269651-218346793
Links
Phenotypes
GenCC
Source:
- paroxysmal nonkinesigenic dyskinesia 1 (Supportive), mode of inheritance: AD
- Tourette syndrome (Limited), mode of inheritance: AD
- paroxysmal nonkinesigenic dyskinesia 1 (Strong), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- Paroxysmal_nonkinesigenic_dyskinesia (483 variants)
- not_provided (100 variants)
- not_specified (62 variants)
- Paroxysmal_nonkinesigenic_dyskinesia_1 (56 variants)
- Inborn_genetic_diseases (50 variants)
- PNKD-related_disorder (18 variants)
- Episodic_hemiplegia (1 variants)
- Paroxysmal_dystonia (1 variants)
- Young-onset_Parkinson_disease (1 variants)
- Paroxysmal_dyskinesia (1 variants)
- Moyamoya_angiopathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNKD gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015488.5. 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 | 85 | 97 | ||||
missense | 265 | 27 | 296 | |||
nonsense | 15 | 15 | ||||
start loss | 1 | 1 | ||||
frameshift | 19 | 20 | ||||
splice donor/acceptor (+/-2bp) | 9 | |||||
Total | 0 | 3 | 316 | 113 | 6 |
Highest pathogenic variant AF is 0.000022309063
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PNKD | protein_coding | protein_coding | ENST00000273077 | 10 | 76402 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.14e-8 | 0.591 | 125681 | 0 | 67 | 125748 | 0.000266 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.323 | 215 | 229 | 0.940 | 0.0000145 | 2413 |
Missense in Polyphen | 56 | 64.772 | 0.86457 | 684 | ||
Synonymous | 1.08 | 80 | 93.3 | 0.857 | 0.00000527 | 823 |
Loss of Function | 1.11 | 14 | 19.2 | 0.728 | 9.19e-7 | 219 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000451 | 0.000451 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000437 | 0.000396 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000197 | 0.000196 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Probable hydrolase that plays an aggravative role in the development of cardiac hypertrophy via activation of the NF-kappa- B signaling pathway. {ECO:0000250}.;
- Disease
- DISEASE: Dystonia 8 (DYT8) [MIM:118800]: A paroxysmal non- kinesigenic dystonia/dyskinesia. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. Dystonia type 8 is characterized by attacks of involuntary movements brought on by stress, alcohol, fatigue or caffeine. The attacks generally last between a few seconds and four hours or longer. The attacks may begin in one limb and spread throughout the body, including the face. {ECO:0000269|PubMed:15262732, ECO:0000269|PubMed:15824259, ECO:0000269|PubMed:16632198, ECO:0000269|PubMed:16717228, ECO:0000269|PubMed:16972263}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.258
Intolerance Scores
- loftool
- 0.156
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 29.31
Haploinsufficiency Scores
- pHI
- 0.512
- hipred
- N
- hipred_score
- 0.224
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pnkd
- Phenotype
- homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione;regulation of synaptic transmission, dopaminergic;regulation of dopamine metabolic process;negative regulation of neurotransmitter secretion;neuromuscular process controlling posture
- Cellular component
- nucleus;mitochondrion;membrane
- Molecular function
- hydroxyacylglutathione hydrolase activity;protein binding;metal ion binding