NM_002354.2(EPCAM):c.859-3C>G AND Lynch syndrome

Clinical significance:Uncertain significance (Last evaluated: May 7, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000198665.1

Allele description [Variation Report for NM_002354.2(EPCAM):c.859-3C>G]

NM_002354.2(EPCAM):c.859-3C>G

Gene:
EPCAM:epithelial cell adhesion molecule [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_002354.2(EPCAM):c.859-3C>G
HGVS:
  • NC_000002.12:g.47385163C>G
  • NG_012352.2:g.45001C>G
  • NM_002354.2:c.859-3C>G
  • LRG_215t1:c.859-3C>G
  • LRG_215:g.45001C>G
  • NC_000002.11:g.47612302C>G
Links:
dbSNP: rs201314303
NCBI 1000 Genomes Browser:
rs201314303
Molecular consequence:
  • NM_002354.2:c.859-3C>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Lynch syndrome
Synonyms:
Familial nonpolyposis colon cancer
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100; OMIM: PS120435

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000254759Invitaecriteria provided, single submitter
Uncertain significance
(May 7, 2015)
germlineclinical testing

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

Summary from all submissions

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

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

Details of each submission

From Invitae, SCV000254759.2

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

Description

This sequence change falls in intron 7 of the EPCAM mRNA. It does not directly change the encoded amino acid sequence of the EPCAM protein. This variant has not been published in the literature and is present in population databases (rs201314303, 0.01%). Algorithms developed to predict the effect of nucleotide changes on mRNA splicing suggest that this intronic variant may alter mRNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, this is a rare intronic change with uncertain impact on splicing. It has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 7, 2021

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