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_004360.4(CDH1):c.1225T>C (p.Trp409Arg)

CA157989

133855 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 26997937-9088-4611-9ef8-bd80077ed64c
Approved on: 2023-08-17
Published on: 2023-08-17

HGVS expressions

NM_004360.4:c.1225T>C
NM_004360.4(CDH1):c.1225T>C (p.Trp409Arg)
NC_000016.10:g.68813400T>C
CM000678.2:g.68813400T>C
NC_000016.9:g.68847303T>C
CM000678.1:g.68847303T>C
NC_000016.8:g.67404804T>C
NG_008021.1:g.81109T>C
ENST00000261769.10:c.1225T>C
ENST00000261769.9:c.1225T>C
ENST00000422392.6:c.1137+1137T>C
ENST00000562836.5:n.1296T>C
ENST00000565810.1:n.269T>C
ENST00000566510.5:c.1069T>C
ENST00000566612.5:c.1225T>C
ENST00000611625.4:c.1225T>C
ENST00000612417.4:c.1225T>C
ENST00000621016.4:c.1225T>C
NM_004360.3:c.1225T>C
NM_001317184.1:c.1137+1137T>C
NM_001317185.1:c.-391T>C
NM_001317186.1:c.-595T>C
NM_004360.5:c.1225T>C
NM_001317184.2:c.1137+1137T>C
NM_001317185.2:c.-391T>C
NM_001317186.2:c.-595T>C
NM_004360.5(CDH1):c.1225T>C (p.Trp409Arg)
More

Likely Benign

Met criteria codes 1
BS2
Not Met criteria codes 25
BP2 BP3 BP1 BP4 BP5 BP7 PS2 PS4 PS1 PS3 PM3 PM1 PM4 PM5 BA1 PM6 PM2 PVS1 PP4 PP1 PP2 PP3 BS4 BS3 BS1

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.1225T>C (p. Trp409Arg) variant has been observed in >10 individuals without a diagnosis of diffuse gastric cancer, signet ring tumor or lobular breast cancer and whose family histories do not suggest HDGC (BS2; internal laboratory contributors). In summary, the clinical significance of this variant is classified as likely benign based on BS2 alone. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2.
Met criteria codes
BS2
Observed in 40 individuals w/o dx HDGC
Not Met criteria codes
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
BP1
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
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
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
PMID: 15235021: increased invasion in collagen gel and impaired cell-cell adhesion in cells transfected with this variant compared to wild type. PMID: 27582386: no effect on cell adhesion in cell culture
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
ExAC - 0.003% 4 allele count (European non-Finnish) gnomAD - 0.002% 5 allele count (European non-Finnish).
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
ExAC - 0.003% 4 allele count (European non-Finnish) gnomAD - 0.002% 5 allele count (European non-Finnish).
PVS1
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
PP2
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
PMID: 15235021: increased invasion in collagen gel and impaired cell-cell adhesion in cells transfected with this variant compared to wild type. PMID: 27582386: no effect on cell adhesion in cell culture
BS1
ExAC - 0.003% 4 allele count (European non-Finnish) gnomAD - 0.002% 5 allele count (European non-Finnish).
Curation History
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