NM_004360.5(CDH1):c.717del (p.Asn240fs) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 9, 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:: RCV003625311.2

Allele description [Variation Report for NM_004360.5(CDH1):c.717del (p.Asn240fs)]

NM_004360.5(CDH1):c.717del (p.Asn240fs)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.717del (p.Asn240fs)

HGVS:

NC_000016.10:g.68810226del
NG_008021.1:g.77935del
NM_001317184.2:c.717del
NM_001317185.2:c.-899del
NM_001317186.2:c.-1103del
NM_004360.5:c.717delMANE SELECT
NP_001304113.1:p.Asn240fs
NP_004351.1:p.Asn240Metfs
NP_004351.1:p.Asn240fs
LRG_301t1:c.717del
LRG_301:g.77935del
LRG_301p1:p.Asn240Metfs
NC_000016.9:g.68844127del
NC_000016.9:g.68844129del
NM_004360.3:c.717delG

Protein change:

N240fs

Molecular consequence:

NM_001317185.2:c.-899del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1103del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.717del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004360.5:c.717del - frameshift variant - [Sequence Ontology: SO:0001589]

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

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Homo sapiens nerve growth factor, beta polypeptide (NGFB), mRNA
Homo sapiens nerve growth factor, beta polypeptide (NGFB), mRNA
gi|4505390|ref|NM_002506.1|

Nucleotide
Homo sapiens dedicator of cytokinesis 8 (DOCK8), RefSeqGene (LRG_196) on chromos...
Homo sapiens dedicator of cytokinesis 8 (DOCK8), RefSeqGene (LRG_196) on chromosome 9
gi|293629236|ref|NG_017007.1||gnl|L G_196

Nucleotide
SLC35F6 [Malurus melanocephalus]
SLC35F6 [Malurus melanocephalus]
Gene ID:130587004

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004489710	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 9, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15235021, 20373070, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004489710

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 9, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline E-cadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria.

Brooks-Wilson AR, Kaurah P, Suriano G, Leach S, Senz J, Grehan N, Butterfield YS, Jeyes J, Schinas J, Bacani J, Kelsey M, Ferreira P, MacGillivray B, MacLeod P, Micek M, Ford J, Foulkes W, Australie K, Greenberg C, LaPointe M, Gilpin C, Nikkel S, et al.

J Med Genet. 2004 Jul;41(7):508-17.

PubMed [citation]

PMID:: 15235021
PMCID:: PMC1735838

Hereditary diffuse gastric cancer: translation of CDH1 germline mutations into clinical practice.

Guilford P, Humar B, Blair V.

Gastric Cancer. 2010 Mar;13(1):1-10. doi: 10.1007/s10120-009-0531-x. Epub 2010 Apr 7. Review.

PubMed [citation]

PMID:: 20373070

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004489710.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CDH1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asn240Metfs*10) in the CDH1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CDH1 are known to be pathogenic (PMID: 15235021, 20373070).

#	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: Sep 29, 2024

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