rs267606712

chr16-68811859-G-Achr16-68811859-G-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The NM_004360.5(CDH1):c.1008G>A(p.Glu336=) variant causes a splice region, synonymous change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CDH1 NM_004360.5 splice_region, synonymous
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:4
• Conservation: PhyloP100: 9.60

Genes affected

CDH1 (HGNC:1748): (cadherin 1) This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 16-68811859-G-A is Pathogenic according to our data. Variant chr16-68811859-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 231647.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH1	NM_004360.5	c.1008G>A	p.Glu336=	splice_region_variant, synonymous_variant	7/16	ENST00000261769.10
CDH1	NM_001317184.2	c.1008G>A	p.Glu336=	splice_region_variant, synonymous_variant	7/15
CDH1	NM_001317185.2	c.-608G>A		splice_region_variant, 5_prime_UTR_variant	7/16
CDH1	NM_001317186.2	c.-812G>A		splice_region_variant, 5_prime_UTR_variant	7/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10	c.1008G>A	p.Glu336=	splice_region_variant, synonymous_variant	7/16	1	NM_004360.5	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary diffuse gastric adenocarcinoma Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Apr 13, 2021	In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with altered splicing, which introduces a premature termination codon (PMID: 8127895, 18427545). The resulting mRNA is expected to undergo nonsense-mediated decay. Studies have shown that this variant alters CDH1 gene expression (PMID: 8127895). This variant has been reported in an observed in individual(s) with diffuse gastric cancer (PMID: 27730413). ClinVar contains an entry for this variant (Variation ID: 231647). This variant is not present in population databases (ExAC no frequency). This sequence change affects codon 336 of the CDH1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the CDH1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jun 12, 2023	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 9537325, Myriad internal data]. -

CDH1-related diffuse gastric and lobular breast cancer syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen CDH1 Variant Curation Expert Panel

Mar 25, 2024

The c.1008G>A (NM_004360.5) variant in CDH1is a G to non-G variant in the last nucleotide in exon 7. It is predicted to cause a loss of the donor splice site resulting in retention of intron 7 (PVS1_Moderate). This prediction is confirmed by RT-PCR cDNA demonstrating that the variant impacts splicing by producing 4 different alternatively spliced transcripts containing premature termination codons (PTC) caused by the use of cryptic donor splice sites in the intron (PS3, PMID: 8127895). This variant has been reported in 4 probands/families meeting hereditary diffuse gastric cancer genetic testing criteria (PS4; PMIDs 9536098, 27730413, ClinVar SCVs: SCV000275557.6, SCV000760854.3, Internal lab contributors). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). The results from 3 in silico splicing predictors (SpliceAI, MaxEntScan, NNsplice) indicate that this variant may affect splicing by disrupting the donor splice site of intron 7 of CDH1 (PP3). 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_Moderate, PM2_Supporting, PS3, PS4, PP3. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 18, 2022

The c.1008G>A pathogenic mutation (also known as p.E336E), located in coding exon 7 of the CDH1 gene, results from a G to A substitution at nucleotide position 1008. This nucleotide substitution does not change the amino acid at codon 336. However, this change occurs in the last base pair of coding exon 7, which makes it likely to have some effect on normal mRNA splicing. This alteration was previously identified in a patient with diffuse gastric cancer (Ambry internal data). It was also observed in a gastric cancer cell line originating from a patient with diffuse gastric cancer (Oda T et al. Proc. Natl. Acad. Sci. U.S.A. 1994 Mar; 91(5):1858-62). RNA analysis of this cell line showed that c.1008G>A abolishes the native donor splice site resulting in three out-of-frame transcripts (Karam R et al. Oncogene 2008 Jul; 27(30):4255-60). Internal RNA splicing analyses of c.1008G>T were consistent with those performed by Karam et al. and showed three out-of-frame transcripts: a 7 base pair insertion, a 25 base pair insertion, and an insertion of intron 7 (Ambry internal data). Additionally, a variant affecting the same nucleotide, c.1008G>T, segregated in a family affected with hereditary diffuse gastric cancer (Guilford P et al. Nature 1998 Mar; 392(6674):402-5). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and may result in the creation or strengthening of a novel splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
Cadd	Uncertain	24
Dann	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.88		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.31		Position offset: 7
DS_DL_spliceai		0.88		Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs267606712; hg19: chr16-68845762; COSMIC: COSV55732029; COSMIC: COSV55732029;