NM_004360.5(CDH1):c.2440-396_*223del AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 1, 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:: RCV003229741.2

Allele description [Variation Report for NM_004360.5(CDH1):c.2440-396_*223del]

NM_004360.5(CDH1):c.2440-396_*223del

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.2440-396_*223del

HGVS:

NC_000016.10:g.68832894_68833722del
NG_008021.1:g.100603_101431del
NM_001317184.2:c.2257-396_*223del
NM_001317185.2:c.892-396_*223del
NM_001317186.2:c.475-396_*223del
NM_004360.5:c.2440-396_*223delMANE SELECT
LRG_301:g.100603_101431del
NC_000016.9:g.68866797_68867625del

Molecular consequence:

NM_001317184.2:c.2257-396_*223del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001317185.2:c.892-396_*223del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001317186.2:c.475-396_*223del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_004360.5:c.2440-396_*223del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Hereditary diffuse gastric adenocarcinoma (HDGC)
Synonyms:: Hereditary diffuse gastric cancer
Identifiers:: MONDO: MONDO:0007648; MedGen: C1708349; Orphanet: 26106; OMIM: 137215

Recent activity

Clear Turn Off Turn On

meiosis 1 arrest protein isoform X7 [Homo sapiens]
meiosis 1 arrest protein isoform X7 [Homo sapiens]
gi|2217325717|ref|XP_047299390.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003926946	European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto - ERN GENTURIS	criteria provided, single submitter (Lee et al. (Hum Mutat. 2018))	Likely pathogenic (Aug 1, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 30311375, 28688938, 36436516

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003926946

European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto - ERN GENTURIS

criteria provided, single submitter

(Lee et al. (Hum Mutat. 2018))

Likely pathogenic
(Aug 1, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants.

Lee K, Krempely K, Roberts ME, Anderson MJ, Carneiro F, Chao E, Dixon K, Figueiredo J, Ghosh R, Huntsman D, Kaurah P, Kesserwan C, Landrith T, Li S, Mensenkamp AR, Oliveira C, Pardo C, Pesaran T, Richardson M, Slavin TP, Spurdle AB, Trapp M, et al.

Hum Mutat. 2018 Nov;39(11):1553-1568. doi: 10.1002/humu.23650.

PubMed [citation]

PMID:: 30311375
PMCID:: PMC6188664

Comparative study of endoscopic surveillance in hereditary diffuse gastric cancer according to CDH1 mutation status.

Mi EZ, Mi EZ, di Pietro M, O'Donovan M, Hardwick RH, Richardson S, Ziauddeen H, Fletcher PC, Caldas C, Tischkowitz M, Ragunath K, Fitzgerald RC.

Gastrointest Endosc. 2018 Feb;87(2):408-418. doi: 10.1016/j.gie.2017.06.028. Epub 2017 Jul 6.

PubMed [citation]

PMID:: 28688938
PMCID:: PMC5780354

See all PubMed Citations (3)

Details of each submission

From European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto - ERN GENTURIS, SCV003926946.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

"1 family fulfilling 2020 HDGC criteria-Familial history of gastric cancer"

PubMed [ID: 28688938]

Description

PVS1_Strong; PS4_Supporting; PM2 (PMID: 30311375)

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

Last Updated: Jun 23, 2024

ClinVar

Relating variation to medicine