NM_004360.5(CDH1):c.269_270delinsCA (p.Arg90Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 11, 2016
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000571292.3

Allele description [Variation Report for NM_004360.5(CDH1):c.269_270delinsCA (p.Arg90Pro)]

NM_004360.5(CDH1):c.269_270delinsCA (p.Arg90Pro)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.269_270delinsCA (p.Arg90Pro)

HGVS:

NC_000016.10:g.68801775_68801776delinsCA
NG_008021.1:g.69484_69485delinsCA
NM_001317184.2:c.269_270delinsCA
NM_001317185.2:c.-1347_-1346delinsCA
NM_001317186.2:c.-1551_-1550delinsCA
NM_004360.5:c.269_270delinsCAMANE SELECT
NP_001304113.1:p.Arg90Pro
NP_004351.1:p.Arg90Pro
LRG_301t1:c.269_270delGGinsCA
LRG_301:g.69484_69485delinsCA
NC_000016.9:g.68835678_68835679delinsCA
NM_004360.3:c.269_270delGGinsCA

Protein change:

R90P

Links:

dbSNP: rs1555514433

NCBI 1000 Genomes Browser:

rs1555514433

Molecular consequence:

NM_001317185.2:c.-1347_-1346delinsCA - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1551_-1550delinsCA - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.269_270delinsCA - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.269_270delinsCA - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000673174	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 11, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000673174

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 11, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV000673174.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.269_270delGGinsCA variant (also known as p.R90P), located in coding exon 3 of the CDH1 gene, results from a deletion of GG and insertion of CA at nucleotide positions 269 and 270. This causes the substitution of the arginine residue at codon 90 for a proline, an amino acid with dissimilar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6498 samples (12996 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.001% (greater than 175000 alleles tested) in our clinical cohort. This amino acid position is poorly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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