chr18-65762981-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004361.5(CDH7):c.139C>T(p.Arg47Cys) variant causes a missense 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 Uncertain significance (★).
Frequency
Consequence
NM_004361.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH7 | NM_004361.5 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 12 | ENST00000397968.4 | NP_004352.2 | |
CDH7 | NM_001362438.2 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 12 | NP_001349367.1 | ||
CDH7 | NM_033646.4 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 12 | NP_387450.1 | ||
CDH7 | NM_001317214.3 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 11 | NP_001304143.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH7 | ENST00000397968.4 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 12 | 1 | NM_004361.5 | ENSP00000381058.2 | ||
CDH7 | ENST00000323011.7 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 12 | 1 | ENSP00000319166.3 | |||
CDH7 | ENST00000536984.6 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 11 | 1 | ENSP00000443030.2 | |||
CDH7 | ENST00000581601.1 | n.-27C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.139C>T (p.R47C) alteration is located in exon 2 (coding exon 1) of the CDH7 gene. This alteration results from a C to T substitution at nucleotide position 139, causing the arginine (R) at amino acid position 47 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at