NM_000038.6(APC):c.3264G>A (p.Lys1088=) AND not specified

Clinical significance:Benign (Last evaluated: Feb 13, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000211908.5

Allele description [Variation Report for NM_000038.6(APC):c.3264G>A (p.Lys1088=)]

NM_000038.6(APC):c.3264G>A (p.Lys1088=)

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.3264G>A (p.Lys1088=)
Other names:
p.K1088K:AAG>AAA
HGVS:
  • NC_000005.10:g.112838858G>A
  • NG_008481.4:g.151338G>A
  • NM_000038.6:c.3264G>AMANE SELECT
  • NM_001127510.3:c.3264G>A
  • NM_001127511.3:c.3210G>A
  • NM_001354895.2:c.3264G>A
  • NM_001354896.2:c.3318G>A
  • NM_001354897.2:c.3294G>A
  • NM_001354898.2:c.3189G>A
  • NM_001354899.2:c.3180G>A
  • NM_001354900.2:c.3141G>A
  • NM_001354901.2:c.3087G>A
  • NM_001354902.2:c.2991G>A
  • NM_001354903.2:c.2961G>A
  • NM_001354904.2:c.2886G>A
  • NM_001354905.2:c.2784G>A
  • NM_001354906.2:c.2415G>A
  • NP_000029.2:p.Lys1088=
  • NP_001120982.1:p.Lys1088=
  • NP_001120983.2:p.Lys1070=
  • NP_001341824.1:p.Lys1088=
  • NP_001341825.1:p.Lys1106=
  • NP_001341826.1:p.Lys1098=
  • NP_001341827.1:p.Lys1063=
  • NP_001341828.1:p.Lys1060=
  • NP_001341829.1:p.Lys1047=
  • NP_001341830.1:p.Lys1029=
  • NP_001341831.1:p.Lys997=
  • NP_001341832.1:p.Lys987=
  • NP_001341833.1:p.Lys962=
  • NP_001341834.1:p.Lys928=
  • NP_001341835.1:p.Lys805=
  • LRG_130:g.151338G>A
  • NC_000005.9:g.112174555G>A
  • NM_000038.5:c.3264G>A
  • p.K1088K
  • p.Lys1088Lys
Links:
dbSNP: rs114774495
NCBI 1000 Genomes Browser:
rs114774495
Molecular consequence:
  • NM_000038.6:c.3264G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127510.3:c.3264G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127511.3:c.3210G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354895.2:c.3264G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354896.2:c.3318G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354897.2:c.3294G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354898.2:c.3189G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354899.2:c.3180G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354900.2:c.3141G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354901.2:c.3087G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354902.2:c.2991G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354903.2:c.2961G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354904.2:c.2886G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354905.2:c.2784G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354906.2:c.2415G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000167005GeneDxcriteria provided, single submitter
Benign
(Mar 10, 2014)
germlineclinical testing

Citation Link,

SCV000600079Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
Benign
(Feb 13, 2017)
germlineclinical testing

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

SCV000691733Mayo Clinic Laboratories, Mayo Clinicno assertion criteria providedLikely benignunknownclinical testing

SCV000805392PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benign
(Jul 20, 2016)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

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 GeneDx, SCV000167005.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000600079.1

#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 Mayo Clinic Laboratories, Mayo Clinic, SCV000691733.1

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

From PreventionGenetics,PreventionGenetics, SCV000805392.1

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

Last Updated: Sep 29, 2021

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