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NM_022089.4(ATP13A2):c.533_536dup (p.Gln179fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 4, 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:
RCV002943346.3

Allele description [Variation Report for NM_022089.4(ATP13A2):c.533_536dup (p.Gln179fs)]

NM_022089.4(ATP13A2):c.533_536dup (p.Gln179fs)

Gene:
ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
1p36.13
Genomic location:
Preferred name:
NM_022089.4(ATP13A2):c.533_536dup (p.Gln179fs)
HGVS:
  • NC_000001.11:g.17004354_17004357dup
  • NG_009054.1:g.12573_12576dup
  • NM_001141973.3:c.518_521dup
  • NM_001141974.3:c.518_521dup
  • NM_022089.4:c.533_536dupMANE SELECT
  • NP_001135445.1:p.Gln174fs
  • NP_001135446.1:p.Gln174fs
  • NP_071372.1:p.Gln179fs
  • LRG_834t1:c.533_536dup
  • LRG_834:g.12573_12576dup
  • LRG_834p1:p.Gln179fs
  • NC_000001.10:g.17330847_17330848insTGGG
  • NC_000001.10:g.17330849_17330852dup
Protein change:
Q174fs
Molecular consequence:
  • NM_001141973.3:c.518_521dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001141974.3:c.518_521dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_022089.4:c.533_536dup - frameshift variant - [Sequence Ontology: SO:0001589]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003275187Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 4, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003275187.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. This sequence change creates a premature translational stop signal (p.Gln179Hisfs*18) 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024