NM_133259.4(LRPPRC):c.1612C>T (p.Gln538Ter) AND Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jun 15, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000667860.2

Allele description [Variation Report for NM_133259.4(LRPPRC):c.1612C>T (p.Gln538Ter)]

NM_133259.4(LRPPRC):c.1612C>T (p.Gln538Ter)

Genes:

LOC129388857:MPRA-validated peak3685 silencer [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.1612C>T (p.Gln538Ter)

HGVS:

NC_000002.12:g.43957422G>A
NG_008247.1:g.43584C>T
NM_133259.4:c.1612C>TMANE SELECT
NP_573566.2:p.Gln538Ter
NC_000002.11:g.44184561G>A
NM_133259.3:c.1612C>T

Protein change:

Q538*

Links:

dbSNP: rs1553406772

NCBI 1000 Genomes Browser:

rs1553406772

Molecular consequence:

NM_133259.4:c.1612C>T - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000792371	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Jun 15, 2017)	unknown	clinical testing	Citation Link,
SCV001162956	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000792371

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Jun 15, 2017)

unknown

clinical testing

Citation Link,

SCV001162956

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Counsyl, SCV000792371.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001162956.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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