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.1312del (p.Thr438fs)

CA658824987

545807 (ClinVar)

Gene: CDH1 (HGNC:999)
Condition: CDH1-related diffuse gastric and lobular breast cancer (MONDO:0007648)
Inheritance Mode: Autosomal dominant inheritance
UUID: b5811c1f-e4fd-48a9-b336-2896da3fd5b9
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.1312del
NM_004360.5(CDH1):c.1312del (p.Thr438fs)
NC_000016.10:g.68813487del
CM000678.2:g.68813487del
NC_000016.9:g.68847390del
CM000678.1:g.68847390del
NC_000016.8:g.67404891del
NG_008021.1:g.81196del
ENST00000261769.10:c.1312del
ENST00000261769.9:c.1312del
ENST00000422392.6:c.1137+1224del
ENST00000562836.5:n.1383del
ENST00000566510.5:c.1156del
ENST00000566612.5:c.1312del
ENST00000611625.4:c.1312del
ENST00000612417.4:c.1312del
ENST00000621016.4:c.1312del
NM_004360.3:c.1312del
NM_001317184.1:c.1137+1224del
NM_001317185.1:c.-304del
NM_001317186.1:c.-508del
NM_004360.4:c.1312del
NM_001317184.2:c.1137+1224del
NM_001317185.2:c.-304del
NM_001317186.2:c.-508del
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Pathogenic

Met criteria codes 3
PM2_Supporting PM5_Supporting PVS1
Not Met criteria codes 23
BA1 BP3 BP4 BP1 BP2 BP7 BP5 BS2 BS3 BS4 BS1 PP3 PP2 PP4 PP1 PS1 PS3 PS2 PS4 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.1312delA p.(Thr438fs) 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.
PM5_Supporting
Exon 9 of 16, predicted NMD.
PVS1
Exon 9 of 16, predicted NMD.
Not Met criteria codes
BA1
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
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
BS2
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
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
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
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
SCV000779091.2 - proband does not meet HDGC phenotype criteria.
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
Curation History
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