NM_022089.4(ATP13A2):c.1459C>T (p.Arg487Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 8, 2023
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:: RCV003767821.3

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1459C>T (p.Arg487Ter)]

NM_022089.4(ATP13A2):c.1459C>T (p.Arg487Ter)

Gene:

ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_022089.4(ATP13A2):c.1459C>T (p.Arg487Ter)

HGVS:

NC_000001.11:g.16996059G>A
NG_009054.1:g.20870C>T
NM_001141973.3:c.1444C>T
NM_001141974.3:c.1444C>T
NM_022089.4:c.1459C>TMANE SELECT
NP_001135445.1:p.Arg482Ter
NP_001135446.1:p.Arg482Ter
NP_071372.1:p.Arg487Ter
LRG_834t1:c.1459C>T
LRG_834:g.20870C>T
LRG_834p1:p.Arg487Ter
NC_000001.10:g.17322554G>A
NM_022089.2:c.1459C>T

Protein change:

R482*

Links:

dbSNP: rs1303653650

NCBI 1000 Genomes Browser:

rs1303653650

Molecular consequence:

NM_001141973.3:c.1444C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001141974.3:c.1444C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_022089.4:c.1459C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Kufor-Rakeb syndrome (KRS)
Synonyms:: Park 9; Pallidopyramidal degeneration with supranuclear upgaze paresis, and dementia; PARKINSON DISEASE 9, AUTOSOMAL RECESSIVE, JUVENILE-ONSET
Identifiers:: MONDO: MONDO:0011706; MedGen: C1847640; Orphanet: 306674; Orphanet: 314632; OMIM: 606693

Name:: Autosomal recessive spastic paraplegia type 78
Identifiers:: MONDO: MONDO:0014975; MedGen: C5567893; OMIM: 617225

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004580383	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 8, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16964263, 21696388, 30746398, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004580383

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 8, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase.

Ramirez A, Heimbach A, Gründemann J, Stiller B, Hampshire D, Cid LP, Goebel I, Mubaidin AF, Wriekat AL, Roeper J, Al-Din A, Hillmer AM, Karsak M, Liss B, Woods CG, Behrens MI, Kubisch C.

Nat Genet. 2006 Oct;38(10):1184-91. Epub 2006 Sep 10.

PubMed [citation]

PMID:: 16964263

Novel mutation in ATP13A2 widens the spectrum of Kufor-Rakeb syndrome (PARK9).

Eiberg H, Hansen L, Korbo L, Nielsen IM, Svenstrup K, Bech S, Pinborg LH, Friberg L, Hjermind LE, Olsen OR, Nielsen JE.

Clin Genet. 2012 Sep;82(3):256-63. doi: 10.1111/j.1399-0004.2011.01745.x. Epub 2011 Jul 18.

PubMed [citation]

PMID:: 21696388

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004580383.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

ClinVar contains an entry for this variant (Variation ID: 520750). This sequence change creates a premature translational stop signal (p.Arg487*) in the ATP13A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP13A2 are known to be pathogenic (PMID: 16964263, 21696388). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Kufor‚ÄêRakeb Syndrome (PMID: 30746398). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

ClinVar

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