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NM_004360.5(CDH1):c.1711+2_1711+7del AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 24, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003328260.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1711+2_1711+7del]

NM_004360.5(CDH1):c.1711+2_1711+7del

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.1711+2_1711+7del
HGVS:
  • NC_000016.10:g.68819427_68819432del
  • NG_008021.1:g.87136_87141del
  • NM_001317184.2:c.1528+2_1528+7del
  • NM_001317185.2:c.163+2_163+7del
  • NM_001317186.2:c.-254-2574_-254-2569del
  • NM_004360.5:c.1711+2_1711+7delMANE SELECT
  • LRG_301t1:c.1711+2_1711+7del
  • LRG_301:g.87136_87141del
  • NC_000016.10:g.68819427_68819432delTAAGGG
  • NC_000016.9:g.68853328_68853333del
  • NC_000016.9:g.68853330_68853335del
  • NM_004360.3:c.1711+2_1711+7del
  • NM_004360.3:c.1711+2_1711+7delTAAGGG
  • NM_004360.4(CDH1):c.1711+2_1711+7delTAAGGG
  • NM_004360.4:c.1711+2_1711+7del
Links:
dbSNP: rs786203089
NCBI 1000 Genomes Browser:
rs786203089
Molecular consequence:
  • NM_001317186.2:c.-254-2574_-254-2569del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1528+2_1528+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001317185.2:c.163+2_163+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_004360.5:c.1711+2_1711+7del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
CDH1-related diffuse gastric and lobular breast cancer syndrome
Synonyms:
CDH1-related diffuse gastric and lobular breast cancer
Identifiers:
MONDO: MONDO:0100488; MedGen: CN311521

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001142272ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely pathogenic
(Aug 24, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen CDH1 Variant Curation Expert Panel, SCV001142272.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.1711+2_1711+7delTAAGGG variant is a canonical splice variant predicted to result in a truncated or absent protein (PVS1_Strong, PM5_Supporting). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). The variant has been reported in at least one family meeting HDGC clinical criteria (PS4_Supporting; SCV000217020.4). In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1_Strong, PM2_Supporting, PS4_Supporting, PM5_Supporting.

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

Last Updated: Sep 29, 2024