NM_133259.4(LRPPRC):c.1432A>G (p.Thr478Ala) AND Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type

Clinical significance:Benign (Last evaluated: May 22, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV001001626.3

Allele description [Variation Report for NM_133259.4(LRPPRC):c.1432A>G (p.Thr478Ala)]

NM_133259.4(LRPPRC):c.1432A>G (p.Thr478Ala)

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.1432A>G (p.Thr478Ala)
Other names:
p.T478A:ACA>GCA
HGVS:
  • NC_000002.12:g.43963644T>C
  • NG_008247.1:g.37362A>G
  • NM_133259.4:c.1432A>GMANE SELECT
  • NP_573566.2:p.Thr478Ala
  • NC_000002.11:g.44190783T>C
  • NM_133259.3:c.1432A>G
  • P42704:p.Thr478Ala
Protein change:
T478A
Links:
UniProtKB: P42704#VAR_052935; dbSNP: rs35035668
NCBI 1000 Genomes Browser:
rs35035668
Molecular consequence:
  • NM_133259.4:c.1432A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type (MC4DN5)
Synonyms:
Leigh syndrome, French Canadian type; Cox deficiency, French Canadian type; Cox deficiency, Saguenay Lac saint Jean type; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009069; MedGen: C1857355; Orphanet: 70472; OMIM: 220111

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000430621Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV001159104ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratoriescriteria provided, single submitter
Benign
(May 22, 2019)
germlineclinical testing

Citation Link,

SCV001452501Natera, Inc.no assertion criteria providedBenign
(Sep 16, 2020)
germlineclinical testing

Summary from all submissions

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

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000430621.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV001159104.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001452501.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2021

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