NM_004360.5(CDH1):c.315del (p.Thr106fs) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 4, 2023
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV003328364.4

Allele description [Variation Report for NM_004360.5(CDH1):c.315del (p.Thr106fs)]

NM_004360.5(CDH1):c.315del (p.Thr106fs)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.315del (p.Thr106fs)

HGVS:

NC_000016.10:g.68801821del
NG_008021.1:g.69530del
NM_001317184.2:c.315del
NM_001317185.2:c.-1301del
NM_001317186.2:c.-1505del
NM_004360.5:c.315delMANE SELECT
NP_001304113.1:p.Thr106fs
NP_004351.1:p.Thr106fs
LRG_301t1:c.315del
LRG_301:g.69530del
NC_000016.10:g.68801821delC
NC_000016.9:g.68835723del
NC_000016.9:g.68835724del
NM_004360.3:c.315delC
NM_004360.4(CDH1):c.315delC
p.Thr106Profs

Protein change:

T106fs

Links:

dbSNP: rs1064795703

NCBI 1000 Genomes Browser:

rs1064795703

Molecular consequence:

NM_001317185.2:c.-1301del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1505del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.315del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004360.5:c.315del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: CDH1-related diffuse gastric and lobular breast cancer syndrome
Synonyms:: CDH1-related diffuse gastric and lobular breast cancer
Identifiers:: MONDO: MONDO:0100488; MedGen: CN311521

Recent activity

Clear Turn Off Turn On

Taxonomy Links for Protein (Select 22218970) (1)
Taxonomy

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
SCV001142230	ClinGen CDH1 Variant Curation Expert Panel	reviewed by expert panel (ClinGen CDH1 ACMG Specifications V3.1)	Pathogenic (Aug 4, 2023)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001142230

ClinGen CDH1 Variant Curation Expert Panel

reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)

Pathogenic
(Aug 4, 2023)

germline

curation

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	curation

Details of each submission

From ClinGen CDH1 Variant Curation Expert Panel, SCV001142230.3

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

Description

The c.315delC p.(Thr106Profs) variant is predicted to result in a premature stop codon that leads to nonsense mediate decay (PVS1 and PM5_supporting). The variant is absent in the gnomAD cohort (PM2_supporting; http://gnomad.broadinstitute.org). Therefore, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (CDH1 VCEP specifications version 3.1): PVS1, PM2_supporting, PM5_supporting.

#	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 26, 2024

ClinVar

Relating variation to medicine