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NM_004360.5(CDH1):c.322del (p.Arg108fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 30, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003182776.2

Allele description [Variation Report for NM_004360.5(CDH1):c.322del (p.Arg108fs)]

NM_004360.5(CDH1):c.322del (p.Arg108fs)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.322del (p.Arg108fs)
HGVS:
  • NC_000016.10:g.68801828del
  • NG_008021.1:g.69537del
  • NM_001317184.2:c.322del
  • NM_001317185.2:c.-1294del
  • NM_001317186.2:c.-1498del
  • NM_004360.4:c.322del
  • NM_004360.5:c.322delMANE SELECT
  • NP_001304113.1:p.Arg108fs
  • NP_004351.1:p.Arg108Glufs
  • NP_004351.1:p.Arg108fs
  • LRG_301t1:c.322del
  • LRG_301:g.69537del
  • LRG_301p1:p.Arg108Glufs
  • NC_000016.9:g.68835731del
  • NM_004360.3:c.322delA
Protein change:
R108fs
Molecular consequence:
  • NM_001317185.2:c.-1294del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1498del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.322del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004360.5:c.322del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003867734Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Nov 30, 2022) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Comparative study of endoscopic surveillance in hereditary diffuse gastric cancer according to CDH1 mutation status.

Mi EZ, Mi EZ, di Pietro M, O'Donovan M, Hardwick RH, Richardson S, Ziauddeen H, Fletcher PC, Caldas C, Tischkowitz M, Ragunath K, Fitzgerald RC.

Gastrointest Endosc. 2018 Feb;87(2):408-418. doi: 10.1016/j.gie.2017.06.028. Epub 2017 Jul 6.

PubMed [citation]
PMID:
28688938
PMCID:
PMC5780354

Details of each submission

From Ambry Genetics, SCV003867734.2

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

Description

The c.322delA variant, located in coding exon 3 of the CDH1 gene, results from a deletion of one nucleotide at nucleotide position 322, causing a translational frameshift with a predicted alternate stop codon (p.R108Efs*9). This alteration has been detected in an individual/family that meets the clinical criteria for Hereditary Diffuse Gastric Cancer (Mi EZ et al. Gastrointest Endosc, 2018 Feb;87:408-418). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

Last Updated: Jun 23, 2024