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NM_022089.4(ATP13A2):c.1039+6C>T AND multiple conditions

Germline classification:
Uncertain significance (3 submissions)
Last evaluated:
Oct 24, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000767898.8

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1039+6C>T]

NM_022089.4(ATP13A2):c.1039+6C>T

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.1039+6C>T
HGVS:
  • NC_000001.11:g.17000005G>A
  • NG_009054.1:g.16924C>T
  • NM_001141973.3:c.1024+6C>T
  • NM_001141974.3:c.1024+6C>T
  • NM_022089.4:c.1039+6C>TMANE SELECT
  • LRG_834t1:c.1039+6C>T
  • LRG_834:g.16924C>T
  • NC_000001.10:g.17326500G>A
  • NM_022089.3:c.1039+6C>T
Links:
dbSNP: rs565724504
NCBI 1000 Genomes Browser:
rs565724504
Molecular consequence:
  • NM_001141973.3:c.1024+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001141974.3:c.1024+6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_022089.4:c.1039+6C>T - intron variant - [Sequence Ontology: SO:0001627]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000898537Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 30, 2021)
germlineclinical testing

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

SCV001233567Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Oct 24, 2022)
germlineclinical testing

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

SCV002805605Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Oct 6, 2021)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (4)

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000898537.2

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

Description

ATP13A2 NM_022089 exon11 c.1039+6C>T: This variant has not been reported in the literature but is present in 10/32884 Latino alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs565724504). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is an intronic variant with no predicted change in the amino acid sequence but may have an unknown effect on splicing. Further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001233567.3

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

Description

This sequence change falls in intron 11 of the ATP13A2 gene. It does not directly change the encoded amino acid sequence of the ATP13A2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs565724504, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 625890). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From Fulgent Genetics, Fulgent Genetics, SCV002805605.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024