PINK1
protein-codingPTEN induced kinase 1, the group of MicroRNA protein coding host genes
Gene summary
This gene encodes a serine/threonine protein kinase that localizes to mitochondria. It is thought to protect cells from stress-induced mitochondrial dysfunction. Mutations in this gene cause one form of autosomal recessive early-onset Parkinson disease. [provided by RefSeq, Jul 2008]
- PARK6
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0011613
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0005180
Submitter: ClinGen
PINK1 was first reported in relation to autosomal-recessive Parkinson´s disease in 2004 (Valente et al. 2004, PMID: 15087508). Parkinson´s disease is a progressive degenerative disorder of the central nervous system characterized by loss of dopamine-producing neurons in the substantia nigra. Signs and symptoms include tremor, which is most pronounced during rest, muscle rigidity, slowing of voluntary movements (bradykinesia), and a tendency to fall back (postural instability). Many pathogenic variants in the biallelic state have been reported in PINK1 in about 200 patients by different authors/groups from different ethnicities (Kasten et al. 2018, PMID: 29644727, www.mdsgene.org). The mutational spectrum is broad, including nonsense, frameshift, splice site, missense changes, and also structural variants (e.g. exon deletions). Fifteen families from five publications are included in this curation, covering patients with biallelic missense or truncating variants. The additional evidence from the literature was not included in this curation because the maximum score for genetic evidence (12 pts.) has been reached. The disease follows a recessive mode of inheritance with seemingly full, age-dependent penetrance. Notably, there is an ongoing debate on the potential role of heterozygous variants as genetic risk factors for Parkinson´s disease (Klein et al. 2007, PMID: 17582365; Hu et al. 2022, PMID: 36305379). The gene-disease association is also supported by recurrent experimental evidence, including animal models and in-vitro functional assays. The mechanism of pathogenicity appears to be a loss-of-function (LOF) indicated by the many truncating variants and further supported by knock-out fly models (Park et al. 2006, PMID: 16672980; Wang et al. 2006, PMID: 16938835). There is a well-defined functional interaction with another autosomal-recessive Parkinson´s disease-linked gene, i.e. PRKN encoding Parkin. While Parkin functions as an E3-ubiquiting ligase for mitochondrial proteins, PINK1 serves as a sensor for disrupted mitochondria (Narendra et al. 2010, PMID: 20126261; Rakovic et al. 2010, PMID: 20508036). It has further repeatedly been shown that several of the PINK1 missense variants impair proper mitophagy (e.g. Kawajiri et al. 2010, PMID: 20153330; Ando et al. 2017, PMID: 28438176). In summary, biallelic, pathogenic variants in PINK1 are definitively causing autosomal-recessive Parkinson´s disease. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time.
Inheritance Pattern: AR
Disease ID:MONDO:0011613
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011613
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0011613
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0017279
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: Neurologic
Rationale: Response to levodopa has been documented
Comments: Heterozygotes may display more subtle signs of disease, and have been described as susceptibility alleles
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PINK1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032409.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 83 | 1 | 92 | ||
| missense | 4 | 7 | 179 | 21 | 1 | 212 |
| nonsense | 10 | 4 | 1 | 15 | ||
| start loss | 0 | |||||
| frameshift | 11 | 8 | 19 | |||
| splice donor/acceptor (+/-2bp) | 2 | 5 | 1 | 8 | ||
| Total | 27 | 24 | 189 | 104 | 2 | 346 |
Highest pathogenic variant AF is 0.00006257535
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115785.1 | 8 | MANE Select | |
| Ensembl | ENSP00000364204.3 | 8 | MANE Select | |
| Ensembl | ENSP00000548798.1 | 8 | Standard | |
| Ensembl | ENSP00000548798.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pink1 | Danio rerio | Structure: dopaminergic neuron Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mitophagy - animal - Homo sapiens (human)
- Parkinson,s disease - Homo sapiens (human)
- Parkinsons Disease Pathway
- Pink/Parkin Mediated Mitophagy
- Mitophagy
Biological Process
- autophagy of mitochondrion
- positive regulation of protein phosphorylation
- regulation of oxidative phosphorylation
- response to ischemia
- protein phosphorylation
Molecular Function
- magnesium ion binding
- protease binding
- protein kinase activity
- protein serine/threonine kinase activity
- protein binding
Cellular Component
- ubiquitin ligase complex
- chromatin
- nucleus
- cytoplasm
- mitochondrion
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000321556
- Coding exons
- 8
- Length
- 18057
- Individuals with no LoFs
- 125630
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 118
- Defined
- 125748
- p
- 0.000469
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.129 | 308 | 314 | 0.980 | 0.0000191 | 3651 |
| Missense (PolyPhen) | 106 | 122.22 | 0.86728 | 1429 | ||
| Synonymous | -1.75 | 166 | 140 | 1.19 | 0.00000926 | 1296 |
| Loss of Function | 1.05 | 18 | 23.5 | 0.766 | 0.00000137 | 253 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00093 | 0.00093 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0010 | 0.0010 | notable |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00035 | 0.00035 | rare |
| South Asian | 0.00039 | 0.00039 | rare |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protects against mitochondrial dysfunction during cellular stress by phosphorylating mitochondrial proteins. Involved in the clearance of damaged mitochondria via selective autophagy (mitophagy) by mediating activation and translocation of PRKN (PubMed:14607334, PubMed:15087508, PubMed:19229105, PubMed:19966284, PubMed:20404107, PubMed:20798600, PubMed:23620051, PubMed:23754282, PubMed:23933751, PubMed:24660806, PubMed:24751536, PubMed:24784582, PubMed:24896179, PubMed:25527291). Targets PRKN to dysfunctional depolarized mitochondria through the phosphorylation of MFN2 (PubMed:23620051). Activates PRKN in 2 steps: (1) by mediating phosphorylation at 'Ser-65' of PRKN and (2) mediating phosphorylation of ubiquitin, converting PRKN to its fully-active form (PubMed:24660806, PubMed:24751536, PubMed:24784582, PubMed:25527291). Required for ubiquinone reduction by mitochondrial complex I by mediating phosphorylation of complex I subunit NDUFA10 (By similarity). {ECO:0000250|UniProtKB:Q99MQ3, ECO:0000269|PubMed:14607334, ECO:0000269|PubMed:15087508, ECO:0000269|PubMed:19229105, ECO:0000269|PubMed:19966284, ECO:0000269|PubMed:20404107, ECO:0000269|PubMed:20798600, ECO:0000269|PubMed:23620051, ECO:0000269|PubMed:23754282, ECO:0000269|PubMed:23933751, ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:24896179, ECO:0000269|PubMed:25527291}.;
- Disease
- DISEASE: Parkinson disease 6 (PARK6) [MIM:605909]: An early-onset form of Parkinson disease, a neurodegenerative disorder characterized by parkinsonian signs such as rigidity, resting tremor and bradykinesia. A subset of patients manifest additional symptoms including hyperreflexia, autonomic instability, dementia and psychiatric disturbances. Symptoms show diurnal fluctuation and can improve after sleep. PARK6 pathogenesis involves respiratory complex I deficiency causing mitochondrial depolarization and dysfunction. Inheritance is autosomal recessive. {ECO:0000269|PubMed:15087508, ECO:0000269|PubMed:15349860, ECO:0000269|PubMed:15349870, ECO:0000269|PubMed:15505171, ECO:0000269|PubMed:15596610, ECO:0000269|PubMed:15955953, ECO:0000269|PubMed:15970950, ECO:0000269|PubMed:16009891, ECO:0000269|PubMed:16207217, ECO:0000269|PubMed:16207731, ECO:0000269|PubMed:16257123, ECO:0000269|PubMed:16401616, ECO:0000269|PubMed:16482571, ECO:0000269|PubMed:16632486, ECO:0000269|PubMed:16966503, ECO:0000269|PubMed:17030667, ECO:0000269|PubMed:18286320, ECO:0000269|PubMed:19229105, ECO:0000269|PubMed:20798600, ECO:0000269|PubMed:22043288, ECO:0000269|PubMed:22956510, ECO:0000269|PubMed:24652937, ECO:0000269|PubMed:24784582}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.176
Intolerance Scores
- LoFtool
- 0.788
- RVIS EVS
- -0.46
- RVIS percentile EVS
- 23.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |