NM_133259.4(LRPPRC):c.1865_1868del (p.Ile622fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Aug 10, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001205402.2

Allele description [Variation Report for NM_133259.4(LRPPRC):c.1865_1868del (p.Ile622fs)]

NM_133259.4(LRPPRC):c.1865_1868del (p.Ile622fs)

Gene:
LRPPRC:leucine rich pentatricopeptide repeat containing [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_133259.4(LRPPRC):c.1865_1868del (p.Ile622fs)
HGVS:
  • NC_000002.12:g.43948176_43948179del
  • NG_008247.1:g.52829_52832del
  • NM_133259.4:c.1865_1868delMANE SELECT
  • NP_573566.2:p.Ile622fs
  • NC_000002.11:g.44175313_44175316del
  • NC_000002.11:g.44175315_44175318del
  • NM_133259.3:c.1865_1868del
  • NM_133259.3:c.1865_1868delTCTA
Protein change:
I622fs
Links:
dbSNP: rs752914914
NCBI 1000 Genomes Browser:
rs752914914
Molecular consequence:
  • NM_133259.4:c.1865_1868del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001376656Invitaecriteria provided, single submitter
Pathogenic
(Aug 10, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

LRPPRC mutations cause early-onset multisystem mitochondrial disease outside of the French-Canadian population.

Oláhová M, Hardy SA, Hall J, Yarham JW, Haack TB, Wilson WC, Alston CL, He L, Aznauryan E, Brown RM, Brown GK, Morris AA, Mundy H, Broomfield A, Barbosa IA, Simpson MA, Deshpande C, Moeslinger D, Koch J, Stettner GM, Bonnen PE, Prokisch H, et al.

Brain. 2015 Dec;138(Pt 12):3503-19. doi: 10.1093/brain/awv291. Epub 2015 Oct 27.

PubMed [citation]
PMID:
26510951
PMCID:
PMC4655343

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001376656.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Ile622Thrfs*16) in the LRPPRC gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs752914914, ExAC 0.01%). This variant has not been reported in the literature in individuals with LRPPRC-related conditions. ClinVar contains an entry for this variant (Variation ID: 554233). Loss-of-function variants in LRPPRC are known to be pathogenic (PMID: 26510951). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 8, 2021

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