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NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe) AND multiple conditions

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 31, 2024
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:
RCV000550501.16

Allele description [Variation Report for NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe)]

NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe)

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.2836A>T (p.Ile946Phe)
HGVS:
  • NC_000001.11:g.16988161T>A
  • NG_009054.1:g.28768A>T
  • NM_001141973.3:c.2821A>T
  • NM_001141974.3:c.2704A>T
  • NM_022089.4:c.2836A>TMANE SELECT
  • NP_001135445.1:p.Ile941Phe
  • NP_001135446.1:p.Ile902Phe
  • NP_071372.1:p.Ile946Phe
  • LRG_834t1:c.2836A>T
  • LRG_834:g.28768A>T
  • LRG_834p1:p.Ile946Phe
  • NC_000001.10:g.17314656T>A
  • NM_022089.2:c.2836A>T
  • NM_022089.3:c.2836A>T
  • Q9NQ11:p.Ile946Phe
Protein change:
I902F
Links:
UniProtKB: Q9NQ11#VAR_058461; dbSNP: rs55708915
NCBI 1000 Genomes Browser:
rs55708915
Molecular consequence:
  • NM_001141973.3:c.2821A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001141974.3:c.2704A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022089.4:c.2836A>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000640194Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Jan 31, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000640194.7

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

Last Updated: Oct 8, 2024