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.1354_1357del (p.Leu452fs)

CA10588623

265543 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9d69b4f3-8f18-42f4-9ad0-719f091202ce
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.1354_1357del
NM_004360.5(CDH1):c.1354_1357del (p.Leu452fs)
NC_000016.10:g.68815548_68815551del
CM000678.2:g.68815548_68815551del
NC_000016.9:g.68849451_68849454del
CM000678.1:g.68849451_68849454del
NC_000016.8:g.67406952_67406955del
NG_008021.1:g.83257_83260del
ENST00000261769.10:c.1354_1357del
ENST00000261769.9:c.1354_1357del
ENST00000422392.6:c.1171_1174del
ENST00000562836.5:n.1425_1428del
ENST00000566510.5:c.*20_*23del
ENST00000566612.5:c.1354_1357del
ENST00000611625.4:c.1417_1420del
ENST00000612417.4:c.1354_1357del
ENST00000621016.4:c.1354_1357del
NM_004360.3:c.1354_1357del
NM_001317184.1:c.1171_1174del
NM_001317185.1:c.-195_-192del
NM_001317186.1:c.-466_-463del
NM_004360.4:c.1354_1357del
NM_001317184.2:c.1171_1174del
NM_001317185.2:c.-195_-192del
NM_001317186.2:c.-466_-463del

Pathogenic

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

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.1354_1357delCTAC p.(Leu452fs) 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
Absent in population databases.
PVS1
Exon 10 of 16, predicted NMD.
PM5_Supporting
Exon 10 of 16, predicted NMD.
Not Met criteria codes
BS3
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
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
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
BP5
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
BP2
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
SCV000322523.8 - Proband 1 Unaffected in 30s (does not meet HDGC criteria); proband 2 Hodgkin's lymphoma (FHx gastric but pathology not confirmed).
BA1
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
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
PM6
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
PM1
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
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