NM_004360.5(CDH1):c.377dup (p.Pro127fs) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 8, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001049836.10

Allele description [Variation Report for NM_004360.5(CDH1):c.377dup (p.Pro127fs)]

NM_004360.5(CDH1):c.377dup (p.Pro127fs)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.377dup (p.Pro127fs)

HGVS:

NC_000016.10:g.68801883dup
NG_008021.1:g.69592dup
NM_001317184.2:c.377dup
NM_001317185.2:c.-1239dup
NM_001317186.2:c.-1443dup
NM_004360.5:c.377dupMANE SELECT
NP_001304113.1:p.Pro127fs
NP_004351.1:p.Pro127fs
LRG_301t1:c.377dup
LRG_301:g.69592dup
NC_000016.9:g.68835780_68835781insC
NC_000016.9:g.68835786dup
NM_004360.3:c.377dup
NM_004360.3:c.377dupC

Protein change:

P127fs

Links:

dbSNP: rs1060501215

NCBI 1000 Genomes Browser:

rs1060501215

Molecular consequence:

NM_001317185.2:c.-1239dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1443dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.377dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004360.5:c.377dup - 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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Burkholderia sp. GB-01 16S ribosomal RNA gene, partial sequence
Burkholderia sp. GB-01 16S ribosomal RNA gene, partial sequence
gi|225346683|gb|FJ793552.1|

Nucleotide
Brachytheciaceae internal transcribed spacer 1, partial sequence; 5.8S ribosomal...
Brachytheciaceae internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence.
PopSet: 157850937

PopSet
Mouse endogenous mammary tumor virus MTV-9 mRNA envelope gene
Mouse endogenous mammary tumor virus MTV-9 mRNA envelope gene
gi|199756|gb|M21800.1|MUSMMTENV

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001213909	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 7, 2019)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15235021, 20373070, 21520333, 28492532
SCV004043532	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jun 8, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001213909

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 7, 2019)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004043532

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Jun 8, 2023)

unknown

clinical testing

Citation Link

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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
not provided	unknown	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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001213909.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Pro127Alafs*41) in the CDH1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in CDH1 are known to be pathogenic (PMID: 15235021, 20373070). This variant has been reported in an individual in the Leiden Open-source Variation Database (PMID: 21520333).

#	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

From Myriad Genetics, Inc., SCV004043532.2

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

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

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

Last Updated: Sep 29, 2024

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