rs34424986
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 8P and 2B. PP5_Very_StrongBP4BS1_Supporting
The NM_004562.3(PRKN):c.823C>T(p.Arg275Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00301 in 1,614,016 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.0022 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0031 ( 9 hom. )
Consequence
PRKN
NM_004562.3 missense
NM_004562.3 missense
Scores
9
6
3
Clinical Significance
Conservation
PhyloP100: 2.05
Genes affected
PRKN (HGNC:8607): (parkin RBR E3 ubiquitin protein ligase) The precise function of this gene is unknown; however, the encoded protein is a component of a multiprotein E3 ubiquitin ligase complex that mediates the targeting of substrate proteins for proteasomal degradation. Mutations in this gene are known to cause Parkinson disease and autosomal recessive juvenile Parkinson disease. Alternative splicing of this gene produces multiple transcript variants encoding distinct isoforms. Additional splice variants of this gene have been described but currently lack transcript support. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PP5
Variant 6-161785820-G-A is Pathogenic according to our data. Variant chr6-161785820-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 7050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-161785820-G-A is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.20339364). . Strength limited to SUPPORTING due to the PP5.
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0031 (4525/1461730) while in subpopulation NFE AF= 0.00375 (4171/1111924). AF 95% confidence interval is 0.00366. There are 9 homozygotes in gnomad4_exome. There are 2196 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PRKN | NM_004562.3 | c.823C>T | p.Arg275Trp | missense_variant | 7/12 | ENST00000366898.6 | NP_004553.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PRKN | ENST00000366898.6 | c.823C>T | p.Arg275Trp | missense_variant | 7/12 | 1 | NM_004562.3 | ENSP00000355865.1 |
Frequencies
GnomAD3 genomes 0.00218 AC: 332AN: 152168Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00194 AC: 486AN: 251096Hom.: 0 AF XY: 0.00191 AC XY: 259AN XY: 135720
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GnomAD4 exome AF: 0.00310 AC: 4525AN: 1461730Hom.: 9 Cov.: 32 AF XY: 0.00302 AC XY: 2196AN XY: 727150
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GnomAD4 genome 0.00218 AC: 332AN: 152286Hom.: 1 Cov.: 33 AF XY: 0.00234 AC XY: 174AN XY: 74462
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:29Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal recessive juvenile Parkinson disease 2 Pathogenic:13Other:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2005 | - - |
| not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Pathogenic and reported on 10-14-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 24, 2017 | The PARK2 c.823C>T (p.Arg275Trp) missense variant is well described as one of the most common PARK2 variants (Hedrich et al. 2004; Mitsuyama et al. 2015). The p.Arg275Trp variant has been reported in at least nine studies in which it was found in over 102 patients with Parkinson disease (primarily with an early-onset phenotype) including one in a homozygous state, 12 in a compound heterozygous state, and 13 in a heterozygous state. Details of zygosity were not given for the remaining individuals (Abbas et al. 1999; Farrer et al. 2001; Lohmann et al. 2003; Hedrich et al. 2004; Klein et al. 2005; Lesage et al. 2008; Li H et al. 2014; Huttenlocher et al. 2015; Mitsuyama et al. 2015). The variant was also found in a heterozygous state in six unaffected individuals and five of 416 controls, while two additional controls were compound heterozygous for the p.Arg275Trp variant and a CNV in the PARK2 gene. The p.Arg275Trp variant is reported at a frequency of 0.0031 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies showed that the variant protein forms intracellular aggregates, is unable to degrade substrates, and results in mitochondrial impairment, in particular reduction in ATP cellular levels (Cookson et al. 2003; Sriram et al. 2005; Zanellati et al. 2015). Based on the collective evidence, the p.Arg275Trp variant is classified as pathogenic for juvenile-onset Parkinson disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 03, 2020 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Centogene AG - the Rare Disease Company | Nov 18, 2019 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Apr 04, 2024 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 13, 2023 | Variant summary: PRKN c.823C>T (p.Arg275Trp) results in a non-conservative amino acid change located in the RING finger domain (IPR047535) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.003 in 1,607,042 control chromosomes in the gnomAD database v4.0 dataset, including 10 homozygotes. However, in gnomAD v4.0 many samples are now derived from large biobanks, which can include individuals with disease. The variant, c.823C>T, has been frequently reported in the literature in homozygous- and compound heterozygous state in individuals affected with Autosomal Recessive Juvenile Parkinson Disease, including families with multiple affected siblings (e.g. Nichols_2002, Khan_2003, Marder_2010, Kim_2021). These data indicate that the variant is very likely to be associated with disease. Several publications reported experimental evidence evaluating an impact on protein function, and demonstrated decreased protein stability with intracellular aggregates, impaired ubiquitination activity, and significantly decreased mitophagy, indicating a clear loss-of-function phenotype (e.g. Sriram_2005, Fiesel_2015, Yi_2019, Broadway_2022). Although the variant has also been reported in (apparent) heterozygous state in several affected individuals, recent large-scale studies examining the role of heterozygous PRKN variants (including R275W) found no association for increased Parkinson Disease risk (e.g. Yu_2021, Zhu_2022). The following publications have been ascertained in the context of this evaluation (PMID: 16049031, 25939424, 30994895, 12114481, 12764051, 20558392, 33497488, 32970363, 35640906, 35954270). 22 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 25, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | Feb 26, 2021 | This sequence change is predicted to replace arginine with tryptophan at codon 275 of the PRKN protein (p.Arg275Trp). The arginine residue is highly conserved (100 vertebrates, UCSC), and located in the RING/Ubox-like zinc-binding domain (Uniprot). There is a large physicochemical difference between arginine and tryptophan. The variant is present in a large population cohort at a frequency of 0.2% (rs34424986, 557/282,496 alleles, 0 homozygotes in gnomAD v2.1). The variant has been identified with a second pathogenic allele in multiple individuals with early-onset Parkinson disease, and segregates with this condition in multiple families (PM3_VeryStrong, PP1_Strong; PMID: 12891670, 22555654, 24831986). The variant causes impaired localisation, mitochondrial ubiquitination, and protein formation in in vitro assays (PS3_Supporting; PMID: 14519684, 24647965, 25939424). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (PP3; 7/7 algorithms). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PP1_Strong, PS3_Supporting, PP3. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | May 21, 2020 | A heterozygous missense variant was identified, NM_004562.2(PRKN):c.823C>T in exon 7 of 12 of the PRKN gene. This substitution is predicted to create a major amino acid change from an arginine to a tryptophan at position 275 of the protein; NP_004553.2(PRKN):p.(Arg275Trp). The arginine at this position has very high conservation (100 vertebrates, UCSC), and is located within the RING finger 1 domain (NCBI, PDB, UniProt). In silico software predicts this variant to be damaging (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD population database at a frequency of 0.2% (557 heterozygotes, 0 homozygotes). This variant has been previously reported as pathogenic and segregated with disease in multiple families with early onset Parkinson’s disease (ClinVar). In addition, functional studies show that this variant causes an aggregation of mutant Parkin protein as large cytoplasmic and nuclear inclusions (Cookson, MR. et al. (2003)) and disrupts glutamatergic synaptic transmission in hippocampal neurons (Zhu, M. et al. (2018)). Based on information available at the time of curation, this variant has been classified as PATHOGENIC. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Mar 24, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | Jun 07, 2019 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Jul 05, 2022 | ACMG classification criteria: PS3 supporting, PM3 very strong, PP1 strong, PP3 supporting - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Dec 19, 2023 | Criteria applied: PM3_VSTR,PS3,PM5_STR,PM1 - |
not provided Pathogenic:10
| Pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 25, 2024 | The frequency of this variant in the general population is consistent with pathogenicity (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). Multiple individuals with early-onset Parkinson disease (EOPD) have been identified with this variant in both the compound heterozygous and heterozygous state. However, the association of heterozygous pathogenic PRKN variants with Parkinson disease remains inconclusive (PMID: 32970363). Assessment of experimental evidence suggests this variant results in abnormal protein function. This variant leads to altered protein localization in the formation of visible aggregates (PMID: 14519684, 16049031, 16714300). In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics Laboratory, Skane University Hospital Lund | May 27, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 18, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 05, 2019 | DNA sequence analysis of the CLN5 gene demonstrated a sequence change, c.556G>A in exon 3, results in an amino acid change, p.Glu186Lys. This sequence change does not appear to have been previously described in patients with CLN5-related disorders and has also not been described as a known benign sequence change in the CLN5 gene. The p.Glu186Lys change affects a highly conserved amino acid residue located in a domain of the CLN5 protein that is not known to be functional. The p.Glu186Lys substitution appears to be possibly damaging using several in-silico pathogenicity prediction tools (SIFT, CADD, Align GVGD, REVEL). - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 21, 2024 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 275 of the PRKN protein (p.Arg275Trp). This variant is present in population databases (rs34424986, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with dementia with Lewy bodies and/or Parkinson's disease (PMID: 10072423, 11889248, 12730996, 12891670, 15390068, 19162522, 19636047, 22118943, 22555654, 24082139, 24831986, 26836416). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 7050). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PRKN protein function. Experimental studies have shown that this missense change affects PRKN function (PMID: 14519684, 16049031, 16714300, 20457763, 25939424). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jul 25, 2023 | Published functional studies show the parkin protein with R275W accumulated around the nucleus in aggregations of misfolded protein, while wild type protein localized primarily to the cytoplasm and nucleus (Cookson et al., 2003); Published functional studies demonstrated that R275W inhibited differentiation of neural stem cells to astrocyte and neurons (Park et al., 2017).; This variant is associated with the following publications: (PMID: 28808173, 25640678, 26556299, 30609409, 27294386, 28656059, 31409571, 22555654, 12730996, 12891670, 20798600, 16049031, 16714300, 14519684, 20457763, 15390068, 19801972, 22118943, 24082139, 19162522, 25591737, 26764160, 25939424, 26683220, 11889248, 10072423, 31324919, 30537300, 30200940, 29353703, 31147223, 27182553, 26855076, 15970950, 26188007, 25907632, 25815004, 24831986, 26836416, 30994895, 33045815, 33504652, 32970363, 34426522, 34434164, 35747619, 28716427, 33818904, 32864185, 33845304, 32740907, 19636047) - |
| Pathogenic, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | Mar 28, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | PRKN: PM3:Very Strong, PP1:Strong, PS3, PM2:Supporting, PM5:Supporting - |
| Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 09, 2023 | PS3, PS4 - |
Young-onset Parkinson disease Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 11, 2020 | The p.Arg275Trp variant in PRKN (also known as PARK2) has been reported in at least 7 compound heterozygous, 2 heterozygous, 1 homozygous and 11 other (unknown zygosity) individuals with early-onset Parkinson disease (Keogh 2016, Zanellati 2015, Mitsuyama 2015, Bognar 2013, Morais 2016, Gorostidi 2016, and Anderson-Mooney 2016), and segregated with disease in 1 affected sibling (Anderson-Mooney 2016). This variant has also been reported in ClinVar (Variation ID 7050) and has been identified in 0.33% (426/128984) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies support that the p.Arg275Trp variant may impact protein function (Bertolin 2015, Fiesel 2015, Cookson 2003, Sriram 2005, and Zanellati 2015). In summary, this variant meets criteria to be classified as pathogenic for early-onset Parkinson disease in an autosomal recessive manner based upon biallelic occurrence in individuals with this disease and supporting functional evidence. ACMG/AMP Criteria applied: PP1, PS3_Moderate, PM3_Very Strong. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 03, 2021 | - - |
PRKN-related disorder Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 31, 2024 | The PRKN c.823C>T variant is predicted to result in the amino acid substitution p.Arg275Trp. This variant (previously denoted as c.924C>T using legacy nomenclature) has been reported in both the homozygous and compound heterozygous states in individuals with early-onset Parkinson disease (see for example Abbas et al. 1999. PubMed ID: 10072423; Oliveira et al. 2003. PubMed ID: 12730996). This variant is considered a founder variant in the European (Non-Finnish) population with an allele frequency of 0.33% (Hedrich et al. 2004. PubMed ID: 15390068). Missense prediction programs classify this amino acid substitution as damaging, and an in vitro functional study found that this substitution decreased the solubility of the PRKN protein (Hampe et al. 2006. PubMed ID: 16714300). This variant has been classified as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/7050/). Given the evidence, we interpret c.823C>T (p.Arg275Trp) as pathogenic. - |
Lung carcinoma;C0919267:Ovarian neoplasm;C1843632:Leprosy, susceptibility to, 2;C1868675:Autosomal recessive juvenile Parkinson disease 2 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Ovarian cancer Pathogenic:1
| Likely pathogenic, no assertion criteria provided | provider interpretation | Solve-RD Consortium | Jun 01, 2022 | Variant confirmed as disease-causing by referring clinical team - |
See cases Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Apr 24, 2019 | This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM3,PP3. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
D;.;.;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Pathogenic
D;D;D;.;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Pathogenic
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D
Polyphen
D;.;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at