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_004360.4(CDH1):c.261delG (p.Arg87Serfs)

CA658658476

463772 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 27459987-4e77-430a-a45a-6fece7004cb7
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.4:c.261delG
NM_004360.4(CDH1):c.261delG (p.Arg87Serfs)
NC_000016.10:g.68801767del
CM000678.2:g.68801767del
NC_000016.9:g.68835670del
CM000678.1:g.68835670del
NC_000016.8:g.67393171del
NG_008021.1:g.69476del
ENST00000261769.10:c.261del
ENST00000261769.9:c.261del
ENST00000422392.6:c.261del
ENST00000561751.1:c.28del
ENST00000562836.5:n.332del
ENST00000564676.5:n.543del
ENST00000564745.1:n.256del
ENST00000566510.5:c.261del
ENST00000566612.5:c.261del
ENST00000611625.4:c.261del
ENST00000612417.4:c.261del
ENST00000621016.4:c.261del
NM_004360.3:c.261del
NM_001317184.1:c.261del
NM_001317185.1:c.-1355del
NM_001317186.1:c.-1559del
NM_004360.4:c.261del
NM_004360.5:c.261del
NM_001317184.2:c.261del
NM_001317185.2:c.-1355del
NM_001317186.2:c.-1559del
NM_004360.5(CDH1):c.261del (p.Arg87fs)

Pathogenic

Met criteria codes 3
PVS1 PM5_Supporting PM2_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 PM1 PM4 PM3 PM6

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.261delG p.(Arg87Serfs) 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
Predicted NMD. Exon 3 of 16.
PM5_Supporting
Predicted NMD. Exon 3 of 16.
PM2_Supporting
Absent in population databases.
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
SCV000637813.2 (Invitae) - proband does not meet HDGC criteria. Not published in the literature.
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
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
PM3
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
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