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.1578G>A (p.Trp526Ter)

CA10588624

265511 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: dffb17c8-bb5d-434c-aefb-9a9dcaef0dc8
Approved on: 2023-08-30
Published on: 2023-08-30

HGVS expressions

NM_004360.5:c.1578G>A
NM_004360.5(CDH1):c.1578G>A (p.Trp526Ter)
NC_000016.10:g.68819292G>A
CM000678.2:g.68819292G>A
NC_000016.9:g.68853195G>A
CM000678.1:g.68853195G>A
NC_000016.8:g.67410696G>A
NG_008021.1:g.87001G>A
ENST00000261769.10:c.1578G>A
ENST00000261769.9:c.1578G>A
ENST00000422392.6:c.1395G>A
ENST00000562836.5:n.1649G>A
ENST00000566510.5:c.*244G>A
ENST00000566612.5:c.1566-2709G>A
ENST00000611625.4:c.1641G>A
ENST00000612417.4:c.1578G>A
ENST00000621016.4:c.1578G>A
NM_004360.3:c.1578G>A
NM_001317184.1:c.1395G>A
NM_001317185.1:c.30G>A
NM_001317186.1:c.-254-2709G>A
NM_004360.4:c.1578G>A
NM_001317184.2:c.1395G>A
NM_001317185.2:c.30G>A
NM_001317186.2:c.-254-2709G>A
More

Pathogenic

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

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.1578G>A p.(Trp526Ter) variant is predicted to result in a premature stop codon that leads to a truncated or absent protein (PVS1, PM5_Supporting). The variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). In summary, 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 (Variant Interpretation Guidelines Version 3.1): PVS1, PM2_Supporting, PM5_Supporting.
Met criteria codes
PVS1
Exon 11 of 16, predicted NMD.
PM2_Supporting
Absent in population databases.
PM5_Supporting
Apply PM5_Supporting to nonsense/frameshift variants that are predicted/proved to undergo NMD.
Not Met criteria codes
BA1
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
Same amino acid change in the c.1577G>A p.(Trp526Ter) variant was reported in a proband meeting the HDGC phenotype criteria, which is an established pathogenic variant (PS1; PMID: 30466290). However, PS1 is not applicable for CDH1.
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
SCV000322481.6 - proband does not meet HGDC criteria. PMID: 30466290 - c.1577G>A p.(Trp526*) in 34 yo with stage IV diffuse gastric ADC (signet ring cell).
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
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
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
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
BP3
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
Curation History
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