rs121964876

chr16-68738318-G-Achr16-68738318-G-Cchr16-68738318-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_004360.5(CDH1):c.70G>A(p.Glu24Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E24D) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CDH1 NM_004360.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.28

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.789

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH1	NM_004360.5	c.70G>A	p.Glu24Lys	missense_variant	2/16	ENST00000261769.10
CDH1	NM_001317184.2	c.70G>A	p.Glu24Lys	missense_variant	2/15
CDH1	NM_001317185.2	c.-1546G>A		5_prime_UTR_variant	2/16
CDH1	NM_001317186.2	c.-1750G>A		5_prime_UTR_variant	2/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH1	ENST00000261769.10	c.70G>A	p.Glu24Lys	missense_variant	2/16	1	NM_004360.5	P1
CDH1	ENST00000422392.6	c.70G>A	p.Glu24Lys	missense_variant	2/15	1
CDH1	ENST00000566612.5	c.70G>A	p.Glu24Lys	missense_variant, NMD_transcript_variant	2/15	1
CDH1	ENST00000566510.5	c.70G>A	p.Glu24Lys	missense_variant, NMD_transcript_variant	2/15	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 05, 2019

The p.E24K variant (also known as c.70G>A), located in coding exon 2 of the CDH1 gene, results from a G to A substitution at nucleotide position 70. The glutamic acid at codon 24 is replaced by lysine, an amino acid with similar properties. This amino acid position is 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	0.12
BayesDel_addAF	Benign	-0.055	T
BayesDel_noAF	Benign	-0.32
Cadd	Benign	19
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.44	T;T;T;.;.
Eigen	Uncertain	0.29
Eigen_PC	Uncertain	0.28
FATHMM_MKL	Benign	0.72	D
LIST_S2	Uncertain	0.89	D;D;D;D;D
M_CAP	Benign	0.042	D
MetaRNN	Pathogenic	0.79	D;D;D;D;D
MetaSVM	Benign	-0.79	T
MutationAssessor	Uncertain	2.4	M;.;.;.;M
MutationTaster	Benign	0.92	N;N
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-1.2	N;.;.;.;N
REVEL	Benign	0.20
Sift	Benign	0.30	T;.;.;.;T
Sift4G	Benign	0.24	T;T;T;T;T
Polyphen		0.73	P;.;.;.;.
Vest4		0.67
MutPred		0.66		Gain of methylation at E24 (P = 0.0066);Gain of methylation at E24 (P = 0.0066);Gain of methylation at E24 (P = 0.0066);Gain of methylation at E24 (P = 0.0066);Gain of methylation at E24 (P = 0.0066);
MVP		0.83
MPC		0.47
ClinPred		0.89	D
GERP RS		4.8
Varity_R		0.12
gMVP		0.41

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

LitVar

Other links and lift over

dbSNP: rs121964876; hg19: chr16-68772221;