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NM_004360.5(CDH1):c.2474C>T (p.Pro825Leu) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Mar 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000478861.12

Allele description [Variation Report for NM_004360.5(CDH1):c.2474C>T (p.Pro825Leu)]

NM_004360.5(CDH1):c.2474C>T (p.Pro825Leu)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.2474C>T (p.Pro825Leu)
HGVS:
  • NC_000016.10:g.68833324C>T
  • NG_008021.1:g.101033C>T
  • NM_001317184.2:c.2291C>T
  • NM_001317185.2:c.926C>T
  • NM_001317186.2:c.509C>T
  • NM_004360.5:c.2474C>TMANE SELECT
  • NP_001304113.1:p.Pro764Leu
  • NP_001304114.1:p.Pro309Leu
  • NP_001304115.1:p.Pro170Leu
  • NP_004351.1:p.Pro825Leu
  • LRG_301t1:c.2474C>T
  • LRG_301:g.101033C>T
  • NC_000016.9:g.68867227C>T
  • NM_004360.3:c.2474C>T
  • NM_004360.4:c.2474C>T
  • p.P825L
Protein change:
P170L
Links:
dbSNP: rs587781312
NCBI 1000 Genomes Browser:
rs587781312
Molecular consequence:
  • NM_001317184.2:c.2291C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.926C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.509C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2474C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000564840GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Mar 1, 2024)
germlineclinical testing

Citation Link,

SCV001134081Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Uncertain significance
(Nov 11, 2022)
unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

New Pathogenic Germline Variants in Very Early Onset and Familial Colorectal Cancer Patients.

Djursby M, Madsen MB, Frederiksen JH, Berchtold LA, Therkildsen C, Willemoe GL, Hasselby JP, Wikman F, Okkels H, Skytte AB, Nilbert M, Wadt K, Gerdes AM, van Overeem Hansen T.

Front Genet. 2020;11:566266. doi: 10.3389/fgene.2020.566266.

PubMed [citation]
PMID:
33193653
PMCID:
PMC7541943

Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.

Breast Cancer Association Consortium., Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, Wahlström C, Pooley KA, Parsons MT, Fortuno C, Wang Q, Bolla MK, Dennis J, Keeman R, Alonso MR, Álvarez N, Herraez B, Fernandez V, Núñez-Torres R, Osorio A, Valcich J, Li M, et al.

N Engl J Med. 2021 Feb 4;384(5):428-439. doi: 10.1056/NEJMoa1913948. Epub 2021 Jan 20.

PubMed [citation]
PMID:
33471991
PMCID:
PMC7611105
See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000564840.9

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

Description

Observed in individuals with personal or family history of breast or colorectal cancer in published literature (PMID: 28961279, 25067988, 33193653, 36436516); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28961279, 22980975, 25067988, 35008396, 33193653, 36436516, 15235021, 22850631)

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001134081.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

The frequency of this variant in the general population, 0.000023 (3/129186 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with breast cancer (PMID: 25067988 (2014)), colorectal cancer (PMID: 33193653 (2020)), and cervical adenosarcoma (PMID: 28961279 (2017)). In a large-scale breast cancer association study, the variant was observed in individuals with breast cancer as well as in unaffected individuals (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/CDH1)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

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

Last Updated: Sep 29, 2024