NM_032409.3(PINK1):c.898C>T (p.Pro300Ser) AND Autosomal recessive early-onset Parkinson disease 6

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 2, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002273040.3

Allele description [Variation Report for NM_032409.3(PINK1):c.898C>T (p.Pro300Ser)]

NM_032409.3(PINK1):c.898C>T (p.Pro300Ser)

Genes:

PINK1-AS:PINK1 antisense RNA [Gene - HGNC]
PINK1:PTEN induced kinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.12

Genomic location:

Preferred name:

NM_032409.3(PINK1):c.898C>T (p.Pro300Ser)

HGVS:

NC_000001.11:g.20644611C>T
NG_008164.1:g.16157C>T
NM_032409.3:c.898C>TMANE SELECT
NP_115785.1:p.Pro300Ser
NC_000001.10:g.20971104C>T
NM_032409.2:c.898C>T

Protein change:

P300S

Links:

dbSNP: rs2154533833

NCBI 1000 Genomes Browser:

rs2154533833

Molecular consequence:

NM_032409.3:c.898C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Autosomal recessive early-onset Parkinson disease 6 (PARK6)
Synonyms:: PARKINSON DISEASE 6, EARLY-ONSET; PARKINSON DISEASE 6, MODIFIER OF; PINK1-Related Parkinson Disease
Identifiers:: MONDO: MONDO:0011613; MedGen: C1853833; Orphanet: 2828; OMIM: 605909

Recent activity

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Dunnia sinensis isolate bC5 ribulose-1,5-bisphosphate carboxylase/oxygenase larg...
Dunnia sinensis isolate bC5 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast
gi|161778002|gb|EU145471.1|

Nucleotide
Neurocalyx championii isolate aX37 ribulose-1,5-bisphosphate carboxylase/oxygena...
Neurocalyx championii isolate aX37 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast
gi|161777986|gb|EU145463.1|

Nucleotide
Inositol polyphosphate 5-phosphatase OCRL-1 [Turdus rufiventris]
Inositol polyphosphate 5-phosphatase OCRL-1 [Turdus rufiventris]
gi|1846361156|gb|KAF4795346.1||gnl| YHW|TURU_093812

Protein
LOC124903626 [Homo sapiens]
LOC124903626 [Homo sapiens]
Gene ID:124903626

Gene
Gastric Poorly Cohesive Adenocarcinoma
Gastric Poorly Cohesive Adenocarcinoma

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002557598	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 2, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002557598

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 2, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557598.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Parkinson disease 6, early onset (MIM#605909). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to serine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated protein kinase domain (UniProt). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 23, 2024

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