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NM_022089.4(ATP13A2):c.1589C>T (p.Pro530Leu) AND Autosomal recessive spastic paraplegia type 78

Germline classification:
Uncertain significance (1 submission)
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:
RCV003339767.2

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1589C>T (p.Pro530Leu)]

NM_022089.4(ATP13A2):c.1589C>T (p.Pro530Leu)

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.1589C>T (p.Pro530Leu)
HGVS:
  • NC_000001.11:g.16993789G>A
  • NG_009054.1:g.23140C>T
  • NM_001141973.3:c.1574C>T
  • NM_001141974.3:c.1574C>T
  • NM_022089.4:c.1589C>TMANE SELECT
  • NP_001135445.1:p.Pro525Leu
  • NP_001135446.1:p.Pro525Leu
  • NP_071372.1:p.Pro530Leu
  • LRG_834t1:c.1589C>T
  • LRG_834:g.23140C>T
  • LRG_834p1:p.Pro530Leu
  • NC_000001.10:g.17320284G>A
Protein change:
P525L
Links:
dbSNP: rs2077019285
NCBI 1000 Genomes Browser:
rs2077019285
Molecular consequence:
  • NM_001141973.3:c.1574C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001141974.3:c.1574C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022089.4:c.1589C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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
SCV004047054Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047054.1

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

Description

The missense variant in c.1589C>T (p.Pro530Leu) in ATP13A2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Pro530Leu variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The amino acid Pro at position 530 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by SIFT and the residue is conserved across species. The amino acid change p.Pro530Leu in ATP13A2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance (VUS). In the absence of another reportable variant/CNV, the molecular diagnosis is not confirmed.

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

Last Updated: Sep 29, 2024