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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  • See Evidence submitted by expert panel for details.

Variant: NM_004360.5(CDH1):c.125C>T (p.Pro42Leu)

CA10580073

231745 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 769d2160-06b8-4eb7-894a-450600260917

HGVS expressions

NM_004360.5:c.125C>T
NM_004360.5(CDH1):c.125C>T (p.Pro42Leu)
NC_000016.10:g.68738373C>T
CM000678.2:g.68738373C>T
NC_000016.9:g.68772276C>T
CM000678.1:g.68772276C>T
NC_000016.8:g.67329777C>T
NG_008021.1:g.6082C>T
ENST00000261769.10:c.125C>T
ENST00000261769.9:c.125C>T
ENST00000422392.6:c.125C>T
ENST00000566510.5:c.125C>T
ENST00000566612.5:c.125C>T
ENST00000611625.4:c.125C>T
ENST00000612417.4:c.125C>T
ENST00000621016.4:c.125C>T
NM_004360.3:c.125C>T
NM_001317184.1:c.125C>T
NM_001317185.1:c.-1491C>T
NM_001317186.1:c.-1695C>T
NM_004360.4:c.125C>T
NM_001317184.2:c.125C>T
NM_001317185.2:c.-1491C>T
NM_001317186.2:c.-1695C>T

Likely Benign

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

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
CDH1 VCEP
The c.125C>T (NM_004360.5) variant in CDH1 is a missense variant predicted to cause substitution of Pro by Leu at amino acid 42 (p.Pro42Leu). This variant has been observed in more than 10 heterozygous individuals with no DGC, SRC tumours and whose families do not suggest HDGC (BS2; GeneDx, Invitae, Color). In summary, the CDH1 VCEP classified the variant as likely benign for DGLBCS based on BS2 alone based on the ACMG/AMP criteria applied, as specified by the ClinGen CDH1 VCEP: BS2. (CDH1 VCEP specifications version 3.1; 04/24/2023)
Met criteria codes
BS2
This variant has been observed in more than 10 heterozygous individuals with no DGC, SRC tumours and whose families do not suggest HDGC (BS2; GeneDx, Invitae, Color).
Not Met criteria codes
PVS1
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Variant absent in gnomAD v2.1.1. Variant present in 2 of 143312 alleles in gnomAD v3 (2 of 13658 alleles in Latino population)
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
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
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
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
PS3
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
BA1
Variant absent in gnomAD v2.1.1. Variant present in 2 of 143312 alleles in gnomAD v3 (2 of 13658 alleles in Latino population)
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
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
Variant absent in gnomAD v2.1.1. Variant present in 2 of 143312 alleles in gnomAD v3 (2 of 13658 alleles in Latino population)
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
Approved on: 2023-08-02
Published on: 2023-08-02
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