rs786202290
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_004360.5(CDH1):c.1711G>A(p.Gly571Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G571D) has been classified as Uncertain significance.
Frequency
Consequence
NM_004360.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.1711G>A | p.Gly571Ser | missense_variant, splice_region_variant | 11/16 | ENST00000261769.10 | |
CDH1 | NM_001317184.2 | c.1528G>A | p.Gly510Ser | missense_variant, splice_region_variant | 10/15 | ||
CDH1 | NM_001317185.2 | c.163G>A | p.Gly55Ser | missense_variant, splice_region_variant | 11/16 | ||
CDH1 | NM_001317186.2 | c.-254-2576G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH1 | ENST00000261769.10 | c.1711G>A | p.Gly571Ser | missense_variant, splice_region_variant | 11/16 | 1 | NM_004360.5 | P1 | |
ENST00000563916.1 | n.264-3766C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Familial cancer of breast;C1708349:Hereditary diffuse gastric adenocarcinoma Pathogenic:1
Pathogenic, no assertion criteria provided | research | King Laboratory, University of Washington | Sep 01, 2019 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.1711G>A variant (also known as p.G571S), located in coding exon 11 of the CDH1 gene, results from a G to A substitution at nucleotide position 1711. The amino acid change results in glycine to serine at codon 571, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 11, which makes it likely to have some effect on normal mRNA splicing. This alteration has been detected in a family with a clinical history consistent with hereditary diffuse gastric cancer (Ambry internal data). RNA analysis has shown to cause aberrant splicing in patient-derived lymphoblast cells (Casadei S et al. Proc Natl Acad Sci U S A, 2019 Dec;:). This nucleotide position is completely conserved on sequence alignment. This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive and direct evidence is insufficient at this time (Ambry internal data). In silico splice site analysis for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at