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.173A>T (p.Glu58Val)

CA193402

185930 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: da2cb751-bdae-4d8e-8fd9-4836bb2b9d90

HGVS expressions

NM_004360.5:c.173A>T
NM_004360.5(CDH1):c.173A>T (p.Glu58Val)
NC_000016.10:g.68801679A>T
CM000678.2:g.68801679A>T
NC_000016.9:g.68835582A>T
CM000678.1:g.68835582A>T
NC_000016.8:g.67393083A>T
NG_008021.1:g.69388A>T
ENST00000261769.10:c.173A>T
ENST00000261769.9:c.173A>T
ENST00000422392.6:c.173A>T
ENST00000562836.5:n.244A>T
ENST00000564676.5:n.455A>T
ENST00000564745.1:n.168A>T
ENST00000566510.5:c.173A>T
ENST00000566612.5:c.173A>T
ENST00000611625.4:c.173A>T
ENST00000612417.4:c.173A>T
ENST00000621016.4:c.173A>T
NM_004360.3:c.173A>T
NM_001317184.1:c.173A>T
NM_001317185.1:c.-1443A>T
NM_001317186.1:c.-1647A>T
NM_004360.4:c.173A>T
NM_001317184.2:c.173A>T
NM_001317185.2:c.-1443A>T
NM_001317186.2:c.-1647A>T

Likely Benign

Met criteria codes 2
PM2_Supporting BS2
Not Met criteria codes 24
PM3 PM5 PM1 PM4 PS4 PS2 PS1 PS3 PM6 BA1 PVS1 BP2 BP3 BP4 BP1 BP5 BP7 BS4 BS3 BS1 PP4 PP1 PP3 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
CDH1 VCEP
The c.173A>T (NM_004360.5) variant in CDH1 is a missense variant predicted to cause substitution of Glu by Val at amino acid 58 (p. Glu58Val). This variant has been observed in more than 10 heterozygous individuals with no DGC, SRC tumours or LBC and and whose families do not suggest HDGC of HDGC (BS2; Invitae, GeneDx, Ambry). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). Although there are both pathogenic and benign types of evidence for this variant, the CDH1 VCEP classified the variant as likely benign for DGLBCS based on BS2 alone. (CDH1 VCEP specifications version 3.1; 04/24/2023)
Met criteria codes
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
BS2
This variant has been observed in more than 10 heterozygous individuals with no DGC, SRC tumours or LBC and and whose families do not suggest HDGC of HDGC (BS2; Invitae, GeneDx, Ambry).
Not Met criteria codes
PM3
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
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
PS4
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
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
absent in gnomAD
PVS1
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
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
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
absent in gnomAD
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
Approved on: 2023-08-02
Published on: 2023-08-02
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