Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_004360.5(CDH1):c.2272G>T (p.Glu758Ter)

CA396470014

532441 (ClinVar)

Gene: CDH1 (HGNC:999)
Condition: CDH1-related diffuse gastric and lobular breast cancer (MONDO:0007648)
Inheritance Mode: Autosomal dominant inheritance
UUID: 5192e01b-3541-4d0d-b286-c2f8acf4043f
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.2272G>T
NM_004360.5(CDH1):c.2272G>T (p.Glu758Ter)
NC_000016.10:g.68828281G>T
CM000678.2:g.68828281G>T
NC_000016.9:g.68862184G>T
CM000678.1:g.68862184G>T
NC_000016.8:g.67419685G>T
NG_008021.1:g.95990G>T
ENST00000261769.10:c.2272G>T
ENST00000261769.9:c.2272G>T
ENST00000422392.6:c.2089G>T
ENST00000562118.1:n.490G>T
ENST00000562836.5:n.2343G>T
ENST00000566510.5:c.*938G>T
ENST00000566612.5:c.*512G>T
ENST00000611625.4:c.2335G>T
ENST00000612417.4:c.1853+1727G>T
ENST00000621016.4:c.1866-5922G>T
NM_004360.3:c.2272G>T
NM_001317184.1:c.2089G>T
NM_001317185.1:c.724G>T
NM_001317186.1:c.307G>T
NM_004360.4:c.2272G>T
NM_001317184.2:c.2089G>T
NM_001317185.2:c.724G>T
NM_001317186.2:c.307G>T
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Pathogenic

Met criteria codes 3
PM2_Supporting PM5_Supporting PVS1
Not Met criteria codes 23
BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP5 BP7 PS2 PS3 PS1 PS4 BA1 PP1 PP4 PP3 PP2 PM6 PM3 PM1 PM4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
CDH1 VCEP
The c.2272G>T (p.Lys758Ter) 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.
Met criteria codes
PM2_Supporting
variant absent from gnomAD population database
PM5_Supporting
variant results in premature stop codon
PVS1
variant results in premature stop codon
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
variant absent from gnomAD population database
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
truncating variant
BP4
truncating variant
BP1
truncating variant
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
truncating variant
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
One family does not meet the HDGC clinical criteria (SCV000760780.1)
BA1
variant absent from gnomAD population database
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
truncating variant
PP2
truncating variant
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
truncating variant
Curation History
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