NM_000466.3(PEX1):c.3208-1G>A AND not provided

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Feb 15, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000466.3(PEX1):c.3208-1G>A]


GATAD1:GATA zinc finger domain containing 1 [Gene - OMIM - HGNC]
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000007.14:g.92491503C>T
  • NG_008341.1:g.42029G>A
  • NG_008341.2:g.42029G>A
  • NM_000466.3:c.3208-1G>AMANE SELECT
  • NM_001282677.2:c.3037-1G>A
  • NM_001282678.2:c.2584-1G>A
  • NC_000007.13:g.92120817C>T
  • NM_000466.2:c.3208-1G>A
dbSNP: rs1057517518
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000466.3:c.3208-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001282677.2:c.3037-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001282678.2:c.2584-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000707639EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
(Apr 6, 2017)
germlineclinical testing

Citation Link,

SCV000710583GeneDxcriteria provided, single submitter
Likely pathogenic
(Feb 15, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000707639.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000710583.2

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


The c.3208-1G>A variant in the PEX1 gene has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. This splice site variant destroys the canonical splice acceptor site in intron 20. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.3208-1G>A variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.3208-1G>A as a likely pathogenic variant.

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

Last Updated: Nov 5, 2021

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