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NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs) AND Kufor-Rakeb syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 26, 2023
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:
RCV003234628.2

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs)]

NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs)

Gene:
ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
1p36.13
Genomic location:
Preferred name:
NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs)
HGVS:
  • NC_000001.11:g.16996090_16996111dup
  • NG_009054.1:g.20818_20839dup
  • NM_001141973.3:c.1392_1413dup
  • NM_001141974.3:c.1392_1413dup
  • NM_022089.4:c.1407_1428dupMANE SELECT
  • NP_001135445.1:p.Met472fs
  • NP_001135446.1:p.Met472fs
  • NP_071372.1:p.Met477fs
  • LRG_834t1:c.1407_1428dup
  • LRG_834:g.20818_20839dup
  • LRG_834p1:p.Met477fs
  • NC_000001.10:g.17322585_17322606dup
Protein change:
M472fs
Molecular consequence:
  • NM_001141973.3:c.1392_1413dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001141974.3:c.1392_1413dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_022089.4:c.1407_1428dup - frameshift variant - [Sequence Ontology: SO:0001589]
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
SCV003932448Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 26, 2023) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes11not 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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV003932448.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.1407_1428dup variant is not present in publicly available population databases like 1000 Genomes, ExAC, EVS, gnomAD, Indian Exome Database or our in-house exome database. This variant has neither been published in literature nor reported to clinical databases like in ClinVar, Human Gene Mutation Database (HGMD) or OMIM, in any affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome, Franklin etc predicted this variant to be likely deleterious. This variant causes frameshift at the 477th amino acid position of the original transcript that creates a premature translational stop signal in the altered transcript which may either result in translation of a truncated protein or cause nonsense mediated decay of the mRNA. This patient harbours another heterozygous variant in ATP13A2 gene (c.514C>T).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not provided1not provided

Last Updated: Jul 16, 2023