NM_004360.5(CDH1):c.308G>A (p.Trp103Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 21, 2024
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:: RCV000567076.4

Allele description [Variation Report for NM_004360.5(CDH1):c.308G>A (p.Trp103Ter)]

NM_004360.5(CDH1):c.308G>A (p.Trp103Ter)

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.308G>A (p.Trp103Ter)

HGVS:

NC_000016.10:g.68801814G>A
NG_008021.1:g.69523G>A
NM_001317184.2:c.308G>A
NM_001317185.2:c.-1308G>A
NM_001317186.2:c.-1512G>A
NM_004360.4:c.308G>A
NM_004360.5:c.308G>AMANE SELECT
NP_001304113.1:p.Trp103Ter
NP_004351.1:p.Trp103Ter
LRG_301t1:c.308G>A
LRG_301:g.69523G>A
NC_000016.9:g.68835717G>A
NC_000016.9:g.68835717G>A
NM_004360.3:c.308G>A
NM_004360.4(CDH1):c.308G>A
p.Trp103Ter

Protein change:

W103*

Links:

dbSNP: rs1555514464

NCBI 1000 Genomes Browser:

rs1555514464

Molecular consequence:

NM_001317185.2:c.-1308G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1512G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.308G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_004360.5:c.308G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000669020	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Mar 21, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000669020

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Mar 21, 2024)

germline

clinical testing

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

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

Citations

PubMed

Multigene Panel Testing Increases the Number of Loci Associated with Gastric Cancer Predisposition.

Tedaldi G, Pirini F, Tebaldi M, Zampiga V, Cangini I, Danesi R, Arcangeli V, Ravegnani M, Abou Khouzam R, Molinari C, Oliveira C, Morgagni P, Saragoni L, Bencivenga M, Ulivi P, Amadori D, Martinelli G, Falcini F, Ranzani GN, Calistri D.

Cancers (Basel). 2019 Sep 11;11(9). doi:pii: E1340. 10.3390/cancers11091340.

PubMed [citation]

PMID:: 31514334
PMCID:: PMC6769562

Details of each submission

From Ambry Genetics, SCV000669020.5

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

Description

The p.W103* pathogenic mutation (also known as c.308G>A), located in coding exon 3 of the CDH1 gene, results from a G to A substitution at nucleotide position 308. This changes the amino acid from a tryptophan to a stop codon within coding exon 3. This mutation has been reported in an Italian patient with diffuse gastric cancer diagnosed at age 37 (Tedaldi G et al. Cancers (Basel), 2019 Sep;11:). In addition to the clinical data presented in the literature, 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: Oct 8, 2024

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