NM_004360.5(CDH1):c.2520del (p.Glu841fs) 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:: RCV003229747.2

Allele description [Variation Report for NM_004360.5(CDH1):c.2520del (p.Glu841fs)]

NM_004360.5(CDH1):c.2520del (p.Glu841fs)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.2520del (p.Glu841fs)

HGVS:

NC_000016.10:g.68833370del
NG_008021.1:g.101079del
NM_001317184.2:c.2337del
NM_001317185.2:c.972del
NM_001317186.2:c.555del
NM_004360.5:c.2520delMANE SELECT
NP_001304113.1:p.Glu780fs
NP_001304114.1:p.Glu325fs
NP_001304115.1:p.Glu186fs
NP_004351.1:p.Glu841Lysfs
NP_004351.1:p.Glu841fs
LRG_301t1:c.2520del
LRG_301:g.101079del
LRG_301p1:p.Glu841Lysfs
NC_000016.9:g.68867273del
NM_004360.3:c.2520delC
NM_004360.4:c.2520del

Protein change:

E186fs

Molecular consequence:

NM_001317184.2:c.2337del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001317185.2:c.972del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001317186.2:c.555del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004360.5:c.2520del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

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

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Homo sapiens FERRY endosomal RAB5 effector complex subunit 3 (FERRY3), transcrip...
Homo sapiens FERRY endosomal RAB5 effector complex subunit 3 (FERRY3), transcript variant 6, mRNA
gi|1890253844|ref|NM_001346157.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003926960	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 (2) [See all records that cite these PMIDs] 30311375, 36436516

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003926960

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 (2)
[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

Genotype-first approach to identify associations between CDH1 germline variants and cancer phenotypes: a multicentre study by the European Reference Network on Genetic Tumour Risk Syndromes.

Garcia-Pelaez J, Barbosa-Matos R, Lobo S, Dias A, Garrido L, Castedo S, Sousa S, Pinheiro H, Sousa L, Monteiro R, Maqueda JJ, Fernandes S, Carneiro F, Pinto N, Lemos C, Pinto C, Teixeira MR, Aretz S, Bajalica-Lagercrantz S, Balmaña J, Blatnik A, Benusiglio PR, et al.

Lancet Oncol. 2023 Jan;24(1):91-106. doi: 10.1016/S1470-2045(22)00643-X. Epub 2022 Nov 24. Erratum in: Lancet Oncol. 2023 Jan;24(1):e10. doi: 10.1016/S1470-2045(22)00761-6.

PubMed [citation]

PMID:: 36436516
PMCID:: PMC9810541

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, SCV003926960.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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

PubMed [ID: 36436516]

Description

PVS1_Moderate; 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

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