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NM_022089.4(ATP13A2):c.348-9_351del AND Kufor-Rakeb syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 29, 2013
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:
RCV000191064.1

Allele description [Variation Report for NM_022089.4(ATP13A2):c.348-9_351del]

NM_022089.4(ATP13A2):c.348-9_351del

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.348-9_351del
HGVS:
  • NC_000001.10:g.17331313_17331325del
  • NC_000001.11:g.17004822_17004834del
  • NG_009054.1:g.12099_12111del
  • NM_001141973.3:c.348-9_351del
  • NM_001141974.3:c.348-9_351del
  • NM_022089.4:c.348-9_351delMANE SELECT
  • LRG_834t1:c.348-9_351del
  • LRG_834:g.12099_12111del
  • NC_000001.10:g.17331313_17331325del
  • NC_000001.10:g.17331313_17331325delCAGGCTGGGGAAG
  • NC_000001.10:g.17331317_17331329del
  • NM_022089.2:c.348-9_351del13
Links:
dbSNP: rs749798211
NCBI 1000 Genomes Browser:
rs749798211
Molecular consequence:
  • NM_001141973.3:c.348-9_351del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001141974.3:c.348-9_351del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_022089.4:c.348-9_351del - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000245454Baylor Genetics - Adult_WES
criteria provided, single submitter

(Yang et al. 2013)		Pathogenic
(Jan 29, 2013) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Causasiansgermlineyes11not providednot providednot providedclinical testing

Citations

PubMed

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.

Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, et al.

N Engl J Med. 2013 Oct 17;369(16):1502-11. doi: 10.1056/NEJMoa1306555. Epub 2013 Oct 2.

PubMed [citation]
PMID:
24088041
PMCID:
PMC4211433

Molecular diagnostic experience of whole-exome sequencing in adult patients.

Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZH, Gambin T, Xia F, Person RE, Walkiewicz M, Shaw CA, Sutton VR, Beaudet AL, Muzny D, Eng CM, Yang Y, Gibbs RA, Lupski JR, Boerwinkle E, et al.

Genet Med. 2016 Jul;18(7):678-85. doi: 10.1038/gim.2015.142. Epub 2015 Dec 3.

PubMed [citation]
PMID:
26633545
PMCID:
PMC4892996

Details of each submission

From Baylor Genetics - Adult_WES, SCV000245454.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Causasians1not providednot providedclinical testing
(GTR000508680.4)		 PubMed (2)

Description

This variant includes the the splice acceptor site of intron 4 and the first four nucleotides of exon 5. Because the splice acceptor site is deleted, it is categorized as deleterious according to ACMG guidelines (PMID:18414213). Found with another missense variant (G315R; phase undetermined) in a 54-year-old male with seizures, apraxia, progressive cognitive problems, confusion, speech difficulty, history of stroke.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided
(GTR000508680.4)		1not provided1not provided

Last Updated: Mar 5, 2024