NM_004360.5(CDH1):c.2430del (p.Phe810fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Apr 30, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000484305.1

Allele description [Variation Report for NM_004360.5(CDH1):c.2430del (p.Phe810fs)]

NM_004360.5(CDH1):c.2430del (p.Phe810fs)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.2430del (p.Phe810fs)
Other names:
NM_004360.4(CDH1):c.2430delT
HGVS:
  • NC_000016.10:g.68829788del
  • NG_008021.1:g.97497del
  • NM_001317184.2:c.2247del
  • NM_001317185.2:c.882del
  • NM_001317186.2:c.465del
  • NM_004360.5:c.2430delMANE SELECT
  • NP_001304113.1:p.Phe749fs
  • NP_001304114.1:p.Phe294fs
  • NP_001304115.1:p.Phe155fs
  • NP_004351.1:p.Phe810fs
  • LRG_301t1:c.2430del
  • LRG_301:g.97497del
  • NC_000016.10:g.68829788delT
  • NC_000016.9:g.68863688del
  • NC_000016.9:g.68863691del
  • NM_004360.3:c.2430delT
  • NM_004360.4:c.2430del
  • NM_004360.4:c.2430delT
  • p.F810LFS*6
Protein change:
F155fs
Links:
dbSNP: rs786203752
NCBI 1000 Genomes Browser:
rs786203752
Molecular consequence:
  • NM_001317184.2:c.2247del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001317185.2:c.882del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001317186.2:c.465del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004360.5:c.2430del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000567126GeneDxcriteria provided, single submitter
Pathogenic
(Apr 30, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000567126.4

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

Description

This deletion of one nucleotide in CDH1 is denoted c.2430delT at the cDNA level and p.Phe810LeufsX6 (F810LfsX6) at the protein level. The normal sequence, with the base that is deleted in brackets, is ATTT[delT]ATTG. The deletion causes a frameshift, which changes a Phenylalanine to a Leucine at codon 810, and creates a premature stop codon at position 6 of the new reading frame. This variant has been reported in a family with a diagnosis of Hereditary Diffuse Gastric Cancer (Hansford 2015). We consider this variant to be pathogenic.

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

Last Updated: Sep 29, 2021

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