NM_022089.4(ATP13A2):c.604del (p.His202fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 8, 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:: RCV003098114.3

Allele description [Variation Report for NM_022089.4(ATP13A2):c.604del (p.His202fs)]

NM_022089.4(ATP13A2):c.604del (p.His202fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_022089.4(ATP13A2):c.604del (p.His202fs)

HGVS:

NC_000001.11:g.17002328del
NG_009054.1:g.14602del
NM_001141973.3:c.589del
NM_001141974.3:c.589del
NM_022089.4:c.604delMANE SELECT
NP_001135445.1:p.His197fs
NP_001135446.1:p.His197fs
NP_071372.1:p.His202fs
LRG_834t1:c.604del
LRG_834:g.14602del
LRG_834p1:p.His202fs
NC_000001.10:g.17328822del
NC_000001.10:g.17328823del
NM_022089.2:c.604delC

Protein change:

H197fs

Molecular consequence:

NM_001141973.3:c.589del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001141974.3:c.589del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022089.4:c.604del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003262305	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 8, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16964263, 21696388, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003262305

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 8, 2022)

germline

clinical testing

PubMed (3)
[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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003262305.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is present in population databases (rs758150853, gnomAD 0.03%). This sequence change creates a premature translational stop signal (p.His202Metfs*10) 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 has not been reported in the literature in individuals affected with ATP13A2-related conditions. 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

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