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]
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Variant: NM_004360.5(CDH1):c.1341del (p.Lys447fs)

CA645509535

439040 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: eac3f3c3-6411-4f1e-8bd0-9dd4b76316e8
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.1341del
NM_004360.5(CDH1):c.1341del (p.Lys447fs)
NC_000016.10:g.68815535del
CM000678.2:g.68815535del
NC_000016.9:g.68849438del
CM000678.1:g.68849438del
NC_000016.8:g.67406939del
NG_008021.1:g.83244del
ENST00000261769.10:c.1341del
ENST00000261769.9:c.1341del
ENST00000422392.6:c.1158del
ENST00000562836.5:n.1412del
ENST00000566510.5:c.*7del
ENST00000566612.5:c.1341del
ENST00000611625.4:c.1404del
ENST00000612417.4:c.1341del
ENST00000621016.4:c.1341del
NM_004360.3:c.1341del
NM_001317184.1:c.1158del
NM_001317185.1:c.-208del
NM_001317186.1:c.-479del
NM_004360.4:c.1341del
NM_001317184.2:c.1158del
NM_001317185.2:c.-208del
NM_001317186.2:c.-479del

Pathogenic

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

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.1341del (p.Lys447fs) 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
PVS1
Variant predicted to cause NMD with premature stop at amino acid 454
PM5_Supporting
Variant predicted to cause NMD with premature stop at amino acid 454
PM2_Supporting
Variant absent from gnomAD
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
1 family with multiple reports of gastric cancer, however pathology not confirmed (internal lab contributor).
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Variant absent from gnomAD
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
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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