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

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 21, 2018
Accession:
VCV000187464.11
Variation ID:
187464
Description:
1bp deletion
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NM_004360.5(CDH1):c.2430del (p.Phe810fs)

Allele ID
184466
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
16q22.1
Genomic location
16: 68829785 (GRCh38) GRCh38 UCSC
16: 68863688 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_301t1:c.2430del
NC_000016.10:g.68829788del
NC_000016.9:g.68863691del
... more HGVS
Protein change
F810fs, F155fs, F749fs, F294fs
Other names
NM_004360.4(CDH1):c.2430delT
Canonical SPDI
NC_000016.10:68829784:TTTT:TTT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA197715
dbSNP: rs786203752
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 reviewed by expert panel Nov 21, 2018 RCV000204049.10
Pathogenic 2 criteria provided, multiple submitters, no conflicts Jan 15, 2020 RCV000167195.4
Pathogenic 1 criteria provided, single submitter Apr 30, 2018 RCV000484305.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CDH1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2755 2795

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Nov 21, 2018)
reviewed by expert panel
Method: curation
Hereditary diffuse gastric cancer
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen CDH1 Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000864602.2
Submitted: (Jan 16, 2019)
Evidence details
Publications
PubMed (1)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.2430delT (p.Phe810Leufs*6) variant is predicted to result in a premature stop codon that leads to a truncated protein. However, it is located within the … (more)
Pathogenic
(Mar 21, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000218032.6
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The c.2430delT pathogenic mutation, located in coding exon 15 of the CDH1 gene, results from a deletion of one nucleotide at nucleotide position 2430, causing … (more)
Pathogenic
(Jul 27, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary diffuse gastric cancer
Allele origin: germline
Invitae
Accession: SCV000261293.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change results in a premature translational stop signal in the last exon of the CDH1 gene (p.Phe810Leufs*6). While this is not anticipated to … (more)
Pathogenic
(Apr 30, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000567126.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
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 … (more)
Likely pathogenic
(Feb 16, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary diffuse gastric cancer
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000917127.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: CDH1 c.2430delT (p.Phe810LeufsX6) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Jan 15, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000903747.2
Submitted: (May 19, 2020)
Comment:
This variant deletes 1 nucleotide in exon 15 of the CDH1 gene, creating a frameshift and premature translation stop signal. This variant is expected to … (more)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
A novel de novo <i>CDH1</i> germline variant aids in the classification of carboxy-terminal E-cadherin alterations predicted to escape nonsense-mediated mRNA decay. Krempely K Cold Spring Harbor molecular case studies 2018 PMID: 29798843
Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond. Hansford S JAMA oncology 2015 PMID: 26182300
The importance of E-cadherin binding partners to evaluate the pathogenicity of E-cadherin missense mutations associated to HDGC. Figueiredo J European journal of human genetics : EJHG 2013 PMID: 22850631
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/9eee2198-3726-4f14-81e7-c8c62c01506a - - - -

Text-mined citations for rs786203752...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2021