NM_133259.4(LRPPRC):c.587A>C (p.Asn196Thr) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001354819.1

Allele description [Variation Report for NM_133259.4(LRPPRC):c.587A>C (p.Asn196Thr)]

NM_133259.4(LRPPRC):c.587A>C (p.Asn196Thr)

Gene:
LRPPRC:leucine rich pentatricopeptide repeat containing [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_133259.4(LRPPRC):c.587A>C (p.Asn196Thr)
HGVS:
  • NC_000002.12:g.43977159T>G
  • NG_008247.1:g.23847A>C
  • NM_133259.4:c.587A>CMANE SELECT
  • NP_573566.2:p.Asn196Thr
  • NC_000002.11:g.44204298T>G
  • NM_133259.3:c.587A>C
Protein change:
N196T
Links:
dbSNP: rs199727887
NCBI 1000 Genomes Browser:
rs199727887
Molecular consequence:
  • NM_133259.4:c.587A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001549526Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001549526.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The LRPPRC p.Asn196Thr variant was not identified in the literature nor was it identified in LOVD 3.0. The variant was identified in dbSNP (ID: rs199727887) and ClinVar (classified as a VUS by Counsyl for Leigh syndrome, French Canadian type). The variant was also identified in control databases in 23 of 282530 chromosomes at a frequency of 0.000081 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 20 of 128914 chromosomes (freq: 0.000155), Other in 1 of 7204 chromosomes (freq: 0.000139), African in 1 of 24958 chromosomes (freq: 0.00004) and European (Finnish) in 1 of 25110 chromosomes (freq: 0.00004), but was not observed in the Latino, Ashkenazi Jewish, East Asian or South Asian populations. The p.Asn196 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Oct 8, 2021

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