NM_004360.5(CDH1):c.808T>G (p.Ser270Ala) AND Hereditary diffuse gastric cancer

Clinical significance:Likely benign (Last evaluated: May 23, 2018)

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:
RCV000144457.8

Allele description

NM_004360.5(CDH1):c.808T>G (p.Ser270Ala)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.808T>G (p.Ser270Ala)
Other names:
p.S270A:TCT>GCT
HGVS:
  • NC_000016.10:g.68810317T>G
  • NG_008021.1:g.78026T>G
  • NM_001317184.2:c.808T>G
  • NM_001317185.2:c.-808T>G
  • NM_001317186.2:c.-1012T>G
  • NM_004360.5:c.808T>G
  • NP_001304113.1:p.Ser270Ala
  • NP_004351.1:p.Ser270Ala
  • LRG_301t1:c.808T>G
  • LRG_301:g.78026T>G
  • NC_000016.9:g.68844220T>G
  • NM_004360.3:c.808T>G
  • NM_004360.4:c.808T>G
  • P12830:p.Ser270Ala
  • p.S270A
Protein change:
S270A
Links:
UniProtKB: P12830#VAR_013970; dbSNP: rs587776399
NCBI 1000 Genomes Browser:
rs587776399
Molecular consequence:
  • NM_001317185.2:c.-808T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1012T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.808T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.808T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary diffuse gastric cancer (HDGC)
Identifiers:
MedGen: C1708349; Orphanet: 26106; OMIM: 137215

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000189523Laboratório de Genética Humana e Médica, Universidade Federal do Paráno assertion provideduntestedgermlinenot provided

SCV000254832Invitaecriteria provided, single submitter
Likely benign
(Dec 18, 2017)
germlineclinical testing

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

SCV000398554Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Jun 14, 2016)
germlineclinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV000786564Counsylcriteria provided, single submitter
Likely benign
(May 23, 2018)
unknownclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf

Citation Link

Description

Mutation detected in a sporadic case of diffuse gastric cancer.

SCV000189523

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot provided1not providedliterature only

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Roles for E-cadherin cell surface regulation in cancer.

Petrova YI, Schecterson L, Gumbiner BM.

Mol Biol Cell. 2016 Nov 1;27(21):3233-3244. Epub 2016 Aug 31.

PubMed [citation]
PMID:
27582386
PMCID:
PMC5170857
See all PubMed Citations (4)

Details of each submission

From Laboratório de Genética Humana e Médica, Universidade Federal do Pará, SCV000189523.1

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

Description

Converted during submission to not provided.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot provided1not providednot providednot providednot providednot providednot provided

From Invitae, SCV000254832.6

#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 Illumina Clinical Services Laboratory,Illumina, SCV000398554.2

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

From Counsyl, SCV000786564.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 2, 2019

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