rs864622630
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004360.5(CDH1):c.2602C>A(p.Arg868Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000131 in 152,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R868C) has been classified as Likely benign.
Frequency
Consequence
NM_004360.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.2602C>A | p.Arg868Ser | missense_variant | 16/16 | ENST00000261769.10 | NP_004351.1 | |
CDH1 | NM_001317184.2 | c.2419C>A | p.Arg807Ser | missense_variant | 15/15 | NP_001304113.1 | ||
CDH1 | NM_001317185.2 | c.1054C>A | p.Arg352Ser | missense_variant | 16/16 | NP_001304114.1 | ||
CDH1 | NM_001317186.2 | c.637C>A | p.Arg213Ser | missense_variant | 15/15 | NP_001304115.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH1 | ENST00000261769.10 | c.2602C>A | p.Arg868Ser | missense_variant | 16/16 | 1 | NM_004360.5 | ENSP00000261769.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Sep 20, 2021 | This missense variant replaces arginine with serine at codon 868 of the CDH1 protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/31396 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 21, 2022 | The p.R868S variant (also known as c.2602C>A), located in coding exon 16 of the CDH1 gene, results from a C to A substitution at nucleotide position 2602. The arginine at codon 868 is replaced by serine, an amino acid with dissimilar properties. This alteration has been reported in an individual affected with colorectal cancer (DeRycke MS et al. Mol Genet Genomic Med, 2017 Sep;5:553-569). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
CDH1-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 23, 2024 | The CDH1 c.2602C>A variant is predicted to result in the amino acid substitution p.Arg868Ser. This variant was identified in a screen of individuals with colorectal cancer, but was classified as a variant of uncertain significance (DeRycke MS et al 2017. PubMed ID: 28944238). This variant is reported in 0.011% of alleles in individuals of African descent in gnomAD, and it classified as uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/479500/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Hereditary diffuse gastric adenocarcinoma Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 30, 2023 | ClinVar contains an entry for this variant (Variation ID: 479500). This variant has not been reported in the literature in individuals affected with CDH1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 868 of the CDH1 protein (p.Arg868Ser). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. - |
Familial cancer of breast;C0376358:Malignant tumor of prostate;C1708349:Hereditary diffuse gastric adenocarcinoma;C4551988:Blepharocheilodontic syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology | Oct 12, 2021 | The c.2602C>A variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD). The variant is not present in Indian Exome Database and in our in-house exome database. The variant was earlier reported to ClinVar (Accession: VCV000220695.10) several times as uncertain significance in association with hereditary cancer predisposing syndrome. CDH1 Arg868Cys occurs at a position that is conserved across species and there is a large physicochemical difference between arginine and cysteine. In-silico pathogenicity prediction programs like SIFT, Polyphen-2, MutationTaster2, CADD etc. predicted this variant to be likely disease causing as it may probably damage the protein structure and function. Varsome predicted this variant as VUS with minor pathogenic evidence but these predictions have not been confirmed by published functional studies and it's clinical significance is uncertain. - |
Familial cancer of breast Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at