NM_004360.5(CDH1):c.1840del (p.Ile614fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 17, 2022
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:: RCV003162193.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1840del (p.Ile614fs)]

NM_004360.5(CDH1):c.1840del (p.Ile614fs)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.1840del (p.Ile614fs)

HGVS:

NC_000016.10:g.68822129del
NG_008021.1:g.89838del
NM_001317184.2:c.1657del
NM_001317185.2:c.292del
NM_001317186.2:c.-126del
NM_004360.5:c.1840delMANE SELECT
NP_001304113.1:p.Ile553fs
NP_001304114.1:p.Ile98fs
NP_004351.1:p.Ile614Serfs
NP_004351.1:p.Ile614fs
LRG_301t1:c.1840del
LRG_301:g.89838del
LRG_301p1:p.Ile614Serfs
NC_000016.9:g.68856032del
NM_004360.3:c.1840delA

Protein change:

I553fs

Molecular consequence:

NM_001317186.2:c.-126del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.1657del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001317185.2:c.292del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004360.5:c.1840del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003867724	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Nov 17, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003867724

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Nov 17, 2022)

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, SCV003867724.2

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

Description

The c.1840delA pathogenic mutation, located in coding exon 12 of the CDH1 gene, results from a deletion of one nucleotide at nucleotide position 1840, causing a translational frameshift with a predicted alternate stop codon (p.I614Sfs*17). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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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