16-68815659-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001317185.2(CDH1):​c.-84C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CDH1
NM_001317185.2 5_prime_UTR_premature_start_codon_gain

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.320
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09455562).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDH1NM_004360.5 linkc.1465C>G p.Pro489Ala missense_variant 10/16 ENST00000261769.10 NP_004351.1 P12830-1A0A0U2ZQU7B3GN61

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDH1ENST00000261769.10 linkc.1465C>G p.Pro489Ala missense_variant 10/161 NM_004360.5 ENSP00000261769.4 P12830-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 29, 2023The p.P489A variant (also known as c.1465C>G), located in coding exon 10 of the CDH1 gene, results from a C to G substitution at nucleotide position 1465. The proline at codon 489 is replaced by alanine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.056
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
10
DANN
Benign
0.69
DEOGEN2
Uncertain
0.77
D;T;T;.;.
Eigen
Benign
-0.68
Eigen_PC
Benign
-0.67
FATHMM_MKL
Benign
0.16
N
LIST_S2
Benign
0.83
T;T;T;T;T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.095
T;T;T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.3
L;.;.;.;.
PrimateAI
Benign
0.24
T
PROVEAN
Uncertain
-3.9
D;.;.;.;D
REVEL
Benign
0.068
Sift
Benign
0.71
T;.;.;.;T
Sift4G
Benign
0.89
T;T;T;T;T
Polyphen
0.0040
B;.;.;.;.
Vest4
0.26
MutPred
0.39
Loss of catalytic residue at P488 (P = 0.0096);Loss of catalytic residue at P488 (P = 0.0096);.;Loss of catalytic residue at P488 (P = 0.0096);.;
MVP
0.77
MPC
0.25
ClinPred
0.060
T
GERP RS
3.7
Varity_R
0.027
gMVP
0.24

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-68849562; API