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NM_004360.5(CDH1):c.1697T>C (p.Ile566Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 2, 2020
Accession:
VCV000185204.9
Variation ID:
185204
Description:
single nucleotide variant
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NM_004360.5(CDH1):c.1697T>C (p.Ile566Thr)

Allele ID
184418
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q22.1
Genomic location
16: 68819411 (GRCh38) GRCh38 UCSC
16: 68853314 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.68819411T>C
NC_000016.9:g.68853314T>C
NM_004360.5:c.1697T>C MANE Select NP_004351.1:p.Ile566Thr missense
... more HGVS
Protein change
I566T, I50T, I505T
Other names
-
Canonical SPDI
NC_000016.10:68819410:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
Links
ClinGen: CA191303
dbSNP: rs763292288
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Mar 1, 2020 RCV000206172.7
Uncertain significance 1 criteria provided, single submitter Dec 12, 2018 RCV000218074.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 2, 2020 RCV000164574.6
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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
2747 2787

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 26, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary diffuse gastric cancer
Allele origin: unknown
Counsyl
Accession: SCV000489592.1
Submitted: (Nov 23, 2016)
Evidence details
Uncertain significance
(Dec 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000279925.9
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted CDH1 c.1697T>C at the cDNA level, p.Ile566Thr (I566T) at the protein level, and results in the change of an Isoleucine to … (more)
Likely benign
(Oct 02, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000215232.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Other strong data supporting benign classification
Uncertain significance
(Mar 01, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary diffuse gastric cancer
Allele origin: germline
Invitae
Accession: SCV000260357.8
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces isoleucine with threonine at codon 566 of the CDH1 protein (p.Ile566Thr). The isoleucine residue is moderately conserved and there is a … (more)
Uncertain significance
(Apr 12, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000689478.3
Submitted: (May 19, 2020)
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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs763292288...

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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 Apr 12, 2021