NM_004360.5:c.1786G>T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_004360.5(CDH1):c.1786G>T(p.Glu596*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. E596E) has been classified as Benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004360.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.1786G>T | p.Glu596* | stop_gained | Exon 12 of 16 | ENST00000261769.10 | NP_004351.1 | |
CDH1 | NM_001317184.2 | c.1603G>T | p.Glu535* | stop_gained | Exon 11 of 15 | NP_001304113.1 | ||
CDH1 | NM_001317185.2 | c.238G>T | p.Glu80* | stop_gained | Exon 12 of 16 | NP_001304114.1 | ||
CDH1 | NM_001317186.2 | c.-180G>T | 5_prime_UTR_variant | Exon 11 of 15 | NP_001304115.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Hereditary diffuse gastric adenocarcinoma Pathogenic:1
PVS1; PS4_Supporting; PM2 (PMID: 30311375) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.