rs587782810

Variant names:

• chr16-68829795-GAAGT-G
• rs587782810
• NM_004360.5:c.2439+5_2439+8delGTAA

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_Strong PM2 PP5_Very_Strong

The ENST00000261769.10(CDH1):​c.2438_2439+2delAAGT​(p.Asn814ValfsTer2) variant causes a frameshift, splice donor, splice region, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CDH1 ENST00000261769.10 frameshift, splice_donor, splice_region, intron
• Clinical Significance: Likely pathogenic reviewed by expert panel P:3 U:1
• Conservation: PhyloP100: 9.82

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.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 11 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-68829795-GAAGT-G is Pathogenic according to our data. Variant chr16-68829795-GAAGT-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 142905.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH1	NM_004360.5	c.2439+5_2439+8delGTAA		splice_region_variant, intron_variant	Intron 15 of 15	ENST00000261769.10	NP_004351.1
CDH1	NM_001317184.2	c.2256+5_2256+8delGTAA		splice_region_variant, intron_variant	Intron 14 of 14		NP_001304113.1
CDH1	NM_001317185.2	c.891+5_891+8delGTAA		splice_region_variant, intron_variant	Intron 15 of 15		NP_001304114.1
CDH1	NM_001317186.2	c.474+5_474+8delGTAA		splice_region_variant, intron_variant	Intron 14 of 14		NP_001304115.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH1	ENST00000261769.10	c.2438_2439+2delAAGT	p.Asn814ValfsTer2	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 15 of 16	1	NM_004360.5	ENSP00000261769.4

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary diffuse gastric adenocarcinoma Pathogenic:1 Uncertain:1

Apr 10, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 15 of the CDH1 gene. It does not directly change the encoded amino acid sequence of the CDH1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with diffuse gastric cancer, breast cancer, and/or endometrial cancer (PMID: 26072394, 29798843). ClinVar contains an entry for this variant (Variation ID: 142905). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Aug 01, 2022

European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3; PS4_Supporting; PM2; PP3 (PMID: 30311375) -

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

Sep 25, 2023

ClinGen CDH1 Variant Curation Expert Panel

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The NM_004360.5(CDH1): c.2439+5_2439+8del is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). This variant is predicted to affect splicing by SpliceAI and NNSPLICE (PP3). Additionally, there is an RNA assay demonstrating an abnormal out-of-frame transcript for this variant (PS3, internal laboratory contributors). This variant has also been reported in at least 2 families meeting HDGC clinical criteria (PS4_Moderate; Internal laboratory contributors). In summary, this variant meets criteria to be classified as likely pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PM2_Supporting, PP3, PS3, PS4_Moderate. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Dec 05, 2019

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2439+5_2439+8delGTAA intronic variant is located after coding exon 15 of the CDH1 gene. This variant results from a deletion of 4 nucleotides at positions c.2439+5 to c.2439+8. This alteration was identified in a proband with diffuse gastric cancer and lobular breast cancer (van der Post RS et al. Gastroenterology. 2015 Oct;149(4):897-906.e19). This region is highly conserved through primates but not in all available vertebrate species. Internal RNA studies confirm that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.45		Position offset: -50
DS_DL_spliceai		1.0		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs587782810; hg19: chr16-68863698;