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NM_000287.4(PEX6):c.2663G>C (p.Arg888Pro) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 22, 2024
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:
RCV004526812.3

Allele description [Variation Report for NM_000287.4(PEX6):c.2663G>C (p.Arg888Pro)]

NM_000287.4(PEX6):c.2663G>C (p.Arg888Pro)

Gene:
PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.1
Genomic location:
Preferred name:
NM_000287.4(PEX6):c.2663G>C (p.Arg888Pro)
HGVS:
  • NC_000006.12:g.42965078C>G
  • NG_008370.1:g.19166G>C
  • NG_008396.1:g.9317C>G
  • NM_000287.4:c.2663G>CMANE SELECT
  • NM_001316313.2:c.2399G>C
  • NP_000278.3:p.Arg888Pro
  • NP_001303242.1:p.Arg800Pro
  • NC_000006.11:g.42932816C>G
  • NM_000287.3:c.2663G>C
  • NR_133009.2:n.2447G>C
Protein change:
R800P
Links:
dbSNP: rs267608247
NCBI 1000 Genomes Browser:
rs267608247
Molecular consequence:
  • NM_000287.4:c.2663G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001316313.2:c.2399G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_133009.2:n.2447G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV005039247Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Uncertain significance
(Mar 22, 2024)
germlineclinical testing

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

Citation Link

Summary from all submissions

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

Citations

PubMed

Spectrum of PEX6 mutations in Zellweger syndrome spectrum patients.

Ebberink MS, Kofster J, Wanders RJ, Waterham HR.

Hum Mutat. 2010 Jan;31(1):E1058-70. doi: 10.1002/humu.21153.

PubMed [citation]
PMID:
19877282

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005039247.3

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

Description

Variant summary: PEX6 c.2663G>C (p.Arg888Pro) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251478 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2663G>C has been reported in the literature in at-least one individual affected with Zellweger Syndrome (example: Ebberink_2010). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 19877282). ClinVar contains an entry for this variant (Variation ID: 931051). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Jul 7, 2024