NM_000466.3(PEX1):c.2331C>A (p.Gly777=) AND not specified

Clinical significance:Benign (Last evaluated: Mar 28, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000078920.11

Allele description [Variation Report for NM_000466.3(PEX1):c.2331C>A (p.Gly777=)]

NM_000466.3(PEX1):c.2331C>A (p.Gly777=)

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.2331C>A (p.Gly777=)
HGVS:
  • NC_000007.14:g.92501975G>T
  • NG_008341.1:g.31557C>A
  • NG_008341.2:g.31557C>A
  • NM_000466.3:c.2331C>AMANE SELECT
  • NM_001282677.2:c.2160C>A
  • NM_001282678.2:c.1707C>A
  • NP_000457.1:p.Gly777=
  • NP_001269606.1:p.Gly720=
  • NP_001269607.1:p.Gly569=
  • NC_000007.13:g.92131289G>T
  • NM_000466.2:c.2331C>A
  • NP_000457.1:p.(=)
  • NP_000457.1:p.(=)
  • p.Gly777Gly
Links:
dbSNP: rs10278857
NCBI 1000 Genomes Browser:
rs10278857
Molecular consequence:
  • NM_000466.3:c.2331C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001282677.2:c.2160C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001282678.2:c.1707C>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
19

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
SCV000110780EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Jul 29, 2013)
germlineclinical testing

Citation Link,

SCV000152175Genetic Services Laboratory, University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000304420PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

SCV000540012Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Mar 28, 2016)
germlineclinical testing

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

SCV001743411Diagnostic 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 providedgermlineunknown19not 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

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000110780.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided19not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided19not providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000152175.2

#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, SCV000304420.1

#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 Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000540012.1

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

Description

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 92% of total chromosomes in ExAC

#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, SCV001743411.3

#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 18, 2021

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