NM_000466.3(PEX1):c.2088A>G (p.Ile696Met) AND not specified

Clinical significance:Benign

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000117900.6

Allele description [Variation Report for NM_000466.3(PEX1):c.2088A>G (p.Ile696Met)]

NM_000466.3(PEX1):c.2088A>G (p.Ile696Met)

Gene:
PEX1:peroxisomal biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_000466.3(PEX1):c.2088A>G (p.Ile696Met)
Other names:
NM_000466.2(PEX1):c.2088A>G(p.Ile696Met); NM_001282677.1(PEX1):c.1917A>G(p.Ile639Met); NM_001282678.1(PEX1):c.1464A>G(p.Ile488Met)
HGVS:
  • NC_000007.14:g.92503179T>C
  • NG_008341.1:g.30353A>G
  • NG_008341.2:g.30353A>G
  • NM_000466.3:c.2088A>GMANE SELECT
  • NM_001282677.2:c.1917A>G
  • NM_001282678.2:c.1464A>G
  • NP_000457.1:p.Ile696Met
  • NP_001269606.1:p.Ile639Met
  • NP_001269607.1:p.Ile488Met
  • NC_000007.13:g.92132493T>C
  • NM_000466.2:c.2088A>G
  • O43933:p.Ile696Met
Protein change:
I488M
Links:
UniProtKB: O43933#VAR_034376; dbSNP: rs35996821
NCBI 1000 Genomes Browser:
rs35996821
Molecular consequence:
  • NM_000466.3:c.2088A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282677.2:c.1917A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282678.2:c.1464A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000152174Genetic Services Laboratory, University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000304419PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

SCV001742320Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensusno assertion criteria providedBenigngermlineclinical testing

Summary from all submissions

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

Citations

PubMed

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 Genetic Services Laboratory, University of Chicago, SCV000152174.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From PreventionGenetics,PreventionGenetics, SCV000304419.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001742320.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 7, 2021

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