PINK1

protein-coding

PTEN 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]

Previous symbols:
  • PARK6

MANE transcript

NM_032409.3

Inheritance

AR, AD

ClinVar variants

P:51U:189B:106

Top phenotype

Parkinson disease 6, early onset

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr1:20,633,458-20,651,511

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~18.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autosomal recessive early-onset Parkinson disease 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011613

Submitter: Genomics England PanelApp

Parkinson diseaseDEFINITIVE

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.

autosomal recessive early-onset Parkinson disease 6DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011613

Submitter: Ambry Genetics

autosomal recessive early-onset Parkinson disease 6LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011613

Submitter: Ambry Genetics

autosomal recessive early-onset Parkinson disease 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011613

Submitter: Labcorp Genetics (formerly Invitae)

young-onset Parkinson diseaseSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017279

Submitter: Orphanet

Clinical Genomic Database (CGD)

Parkinson disease 6, early onsetAR

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

Refs: 15505170; 15349870; 15087508; 15955954; 15970950; 16969854; 17030667; 16769864; 16966503; 16632486; 18685134; 18541801; 21784538; 22581678; 22956510Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PINK1 variants in ClinVar

12 Conditions Cataloged
Autosomal recessive early-onset Parkinson disease 6Total: 315
not providedTotal: 118
Inborn genetic diseasesTotal: 50
PINK1-related disorderTotal: 24
not specifiedTotal: 21
Parkinson disease, late-onsetTotal: 2
ischemic cerebrovascular dieseaseTotal: 2
See casesTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
83
clinvar
1
clinvar
92
missense
4
clinvar
7
clinvar
179
clinvar
21
clinvar
1
clinvar
212
nonsense
10
clinvar
4
clinvar
1
clinvar
15
start loss
0
frameshift
11
clinvar
8
clinvar
19
splice donor/acceptor (+/-2bp)
2
clinvar
5
clinvar
1
clinvar
8
Total27241891042346

Highest pathogenic variant AF is 0.00006257535

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_032409.3RefSeqNP_115785.18MANE Select
ENST00000321556.5EnsemblENSP00000364204.38MANE Select
ENST00000878739.1EnsemblENSP00000548798.18Standard
ENST00000878739.2EnsemblENSP00000548798.18Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
pink1Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.1293083140.9800.00001913651
Missense (PolyPhen)106122.220.867281429
Synonymous-1.751661401.190.000009261296
Loss of Function1.051823.50.7660.00000137253

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000930.00093rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.00100.0010notable
Finnish0.000190.00018rare
European (Non-Finnish)0.000350.00035rare
South Asian0.000390.00039rare
Other0.000980.00098rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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