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NM_000287.4(PEX6):c.1841del (p.Leu614fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 13, 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:
RCV001008824.1

Allele description [Variation Report for NM_000287.4(PEX6):c.1841del (p.Leu614fs)]

NM_000287.4(PEX6):c.1841del (p.Leu614fs)

Gene:
PEX6:peroxisomal biogenesis factor 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6p21.1
Genomic location:
Preferred name:
NM_000287.4(PEX6):c.1841del (p.Leu614fs)
HGVS:
  • NC_000006.12:g.42967411del
  • NG_008370.1:g.16833del
  • NM_000287.4:c.1841delMANE SELECT
  • NM_001316313.2:c.1577del
  • NP_000278.3:p.Leu614fs
  • NP_001303242.1:p.Leu526fs
  • NC_000006.11:g.42935149del
  • NC_000006.11:g.42935149del
  • NM_000287.3:c.1841delT
  • NR_133009.2:n.1872del
Protein change:
L526fs
Links:
OMIM: 601498.0013; dbSNP: rs863225083
NCBI 1000 Genomes Browser:
rs863225083
Molecular consequence:
  • NM_000287.4:c.1841del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001316313.2:c.1577del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_133009.2:n.1872del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001168627GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Dec 13, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168627.1

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

Description

The c.1841delT variant in the PEX6 gene has been reported previously in twin siblings with Heimler syndrome who also harbored a PEX6 missense variant, although parental studies were not performed to determine the phase of these two variants (Ratbi et al., 2015). Functional studies using in vitro transfection of the c.1841delT variant showed minimal functional complementation of peroxisome biogenesis in peroxisome deficient cells. The c.1841delT variant causes a frameshift starting with codon Leucine 614, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 5 of the new reading frame, denoted p.Leu614ArgfsX5. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1841delT variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.1841delT as a pathogenic variant.

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

Last Updated: Feb 20, 2024