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NM_006660.5(CLPX):c.893G>A (p.Gly298Asp) AND Protoporphyria, erythropoietic, 2

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Oct 15, 2018
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:
RCV000656530.1

Allele description [Variation Report for NM_006660.5(CLPX):c.893G>A (p.Gly298Asp)]

NM_006660.5(CLPX):c.893G>A (p.Gly298Asp)

Gene:
CLPX:caseinolytic mitochondrial matrix peptidase chaperone subunit X [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q22.31
Genomic location:
Preferred name:
NM_006660.5(CLPX):c.893G>A (p.Gly298Asp)
HGVS:
  • NC_000015.10:g.65157910C>T
  • NM_006660.5:c.893G>AMANE SELECT
  • NP_006651.2:p.Gly298Asp
  • NC_000015.9:g.65450248C>T
  • NM_006660.4:c.893G>A
  • NR_133680.2:n.970G>A
Protein change:
G298D; GLY298ASP
Links:
OMIM: 615611.0001; dbSNP: rs1555412542
NCBI 1000 Genomes Browser:
rs1555412542
Molecular consequence:
  • NM_006660.5:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_133680.2:n.970G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Protoporphyria, erythropoietic, 2 (EPP2)
Identifiers:
MONDO: MONDO:0060729; MedGen: C4693947; OMIM: 618015

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000778542OMIM
no assertion criteria provided
Pathogenic
(Jun 19, 2018)
germlineliterature only

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

SCV000883295SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 15, 2018)
unknowncuration

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedcuration
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutation in human CLPX elevates levels of δ-aminolevulinate synthase and protoporphyrin IX to promote erythropoietic protoporphyria.

Yien YY, Ducamp S, van der Vorm LN, Kardon JR, Manceau H, Kannengiesser C, Bergonia HA, Kafina MD, Karim Z, Gouya L, Baker TA, Puy H, Phillips JD, Nicolas G, Paw BH.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):E8045-E8052. doi: 10.1073/pnas.1700632114. Epub 2017 Sep 5.

PubMed [citation]
PMID:
28874591
PMCID:
PMC5617249

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 OMIM, SCV000778542.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In an 18-year-old French girl with erythropoietic porphyria-2 (EPP2; 618015), Yien et al. (2017) identified a heterozygous c.1102G-A transition (c.1102G-A, NM_006660) at the exon 7 splice junction border of the CLPX gene, resulting in a gly298-to-asp (G298D) substitution at a highly conserved residue in the Walker A motif that forms part of the ATP-binding pocket. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the gnomAD database. The patient's father and paternal uncle, who had milder forms of the disorder, also carried the mutation. In vitro functional expression studies showed that the G298D mutant CLPX protein lacked detectable ATPase activity compared to wildtype, and partially suppressed the ATPase of wildtype CLPX promoters, consistent with a dominant-negative effect. Cells with the mutant protein showed impaired CLPX-dependent turnover of ALAS, resulting in increased posttranslational stability of ALAS (ALAS1, 125290 and ALAS2, 301300) and pathologic accumulation of the heme biosynthesis intermediate protoporphyrin IX (PPIX). Erythroid cells from the patient showed modestly increased levels of ALAS2, and CRISPR-mediated disruption of CLPX caused increased ALAS1 protein levels.

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

From SIB Swiss Institute of Bioinformatics, SCV000883295.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)

Description

This variant is interpreted as Likely Pathogenic, for Protoporphyria, erythropoietic, 2, autosomal dominant. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM1 => Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation (https://www.uniprot.org/uniprot/O76031). PS3 => Well-established functional studies show a deleterious effect (https://www.ncbi.nlm.nih.gov/pubmed/28874591).

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

Last Updated: Apr 23, 2022