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NM_004360.5(CDH1):c.1685C>G (p.Thr562Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Nov 30, 2020)
Last evaluated:
Apr 5, 2019
Accession:
VCV000142321.6
Variation ID:
142321
Description:
single nucleotide variant
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NM_004360.5(CDH1):c.1685C>G (p.Thr562Arg)

Allele ID
152035
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q22.1
Genomic location
16: 68819399 (GRCh38) GRCh38 UCSC
16: 68853302 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_301:g.87108C>G
NC_000016.9:g.68853302C>G
NC_000016.10:g.68819399C>G
... more HGVS
Protein change
T562R, T46R, T501R
Other names
-
Canonical SPDI
NC_000016.10:68819398:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA168064
dbSNP: rs587782381
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Aug 29, 2018 RCV000791845.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 5, 2019 RCV000131384.5
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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
2711 2751

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 29, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary diffuse gastric cancer
Allele origin: germline
Invitae
Accession: SCV000931111.1
Submitted: (Mar 28, 2019)
Evidence details
Comment:
This sequence change replaces threonine with arginine at codon 562 of the CDH1 protein (p.Thr562Arg). The threonine residue is moderately conserved and there is a … (more)
Uncertain significance
(Apr 05, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000684374.3
Submitted: (May 19, 2020)
Evidence details
Likely benign
(Jul 29, 2013)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000186360.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;In silico models in agreement (benign)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs587782381...

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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 Feb 03, 2021