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NM_004360.5(CDH1):c.2412C>T (p.Pro804=) AND not provided

Germline classification:
Benign/Likely benign (3 submissions)
Last evaluated:
Jun 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:
RCV000757066.19

Allele description [Variation Report for NM_004360.5(CDH1):c.2412C>T (p.Pro804=)]

NM_004360.5(CDH1):c.2412C>T (p.Pro804=)

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.2412C>T (p.Pro804=)
HGVS:
  • NC_000016.10:g.68829770C>T
  • NG_008021.1:g.97479C>T
  • NM_001317184.2:c.2229C>T
  • NM_001317185.2:c.864C>T
  • NM_001317186.2:c.447C>T
  • NM_004360.5:c.2412C>TMANE SELECT
  • NP_001304113.1:p.Pro743=
  • NP_001304114.1:p.Pro288=
  • NP_001304115.1:p.Pro149=
  • NP_004351.1:p.Pro804=
  • LRG_301t1:c.2412C>T
  • LRG_301:g.97479C>T
  • NC_000016.9:g.68863673C>T
  • NM_004360.3:c.2412C>T
  • NM_004360.4:c.2412C>T
  • p.P804P
  • p.Pro804Pro
Links:
dbSNP: rs202075199
NCBI 1000 Genomes Browser:
rs202075199
Molecular consequence:
  • NM_001317184.2:c.2229C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317185.2:c.864C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317186.2:c.447C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004360.5:c.2412C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

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
SCV000885155ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)
Likely benign
(Feb 7, 2018)
germlineclinical testing

Citation Link,

SCV000889250Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Benign
(Aug 4, 2022)
unknownclinical testing

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

SCV002497926CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Jun 1, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885155.1

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

Description

The CDH1 c.2412C>T; p.Pro804Pro variant (rs202075199), to our knowledge, is not reported in the medical literature but is classified as benign or likely benign in ClinVar (Variation ID: 183811). This variant is found in the general population with an overall allele frequency of 0.008% (21/277046 alleles) in the Genome Aggregation Database. This is a synonymous change, the nucleotide is not conserved, and computational algorithms do not predict this variant to impact splicing (Alamut v.2.10). Based on available information, this variant is considered likely benign.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000889250.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV002497926.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

CDH1: BP4, BP7

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Jul 15, 2024