rs896586706

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001220488.2(CDH13):​c.50T>A​(p.Leu17His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,453,490 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

CDH13
NM_001220488.2 missense

Scores

1
4
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.57
Variant links:
Genes affected
CDH13 (HGNC:1753): (cadherin 13) This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDH13NM_001257.5 linkc.15T>A p.Thr5Thr synonymous_variant Exon 1 of 14 ENST00000567109.6 NP_001248.1 P55290-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDH13ENST00000567109.6 linkc.15T>A p.Thr5Thr synonymous_variant Exon 1 of 14 1 NM_001257.5 ENSP00000479395.1 P55290-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.88e-7
AC:
1
AN:
1453490
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
722090
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.020
T
BayesDel_noAF
Benign
-0.27
CADD
Benign
14
DANN
Benign
0.97
Eigen
Uncertain
0.21
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Benign
0.67
D
LIST_S2
Benign
0.23
T
M_CAP
Benign
0.075
D
MetaRNN
Uncertain
0.54
D
MetaSVM
Benign
-0.87
T
PrimateAI
Uncertain
0.51
T
PROVEAN
Benign
0.18
N
REVEL
Benign
0.094
Sift
Pathogenic
0.0
D
Vest4
0.65
MutPred
0.17
Loss of stability (P = 0.0153);
MVP
0.80
MPC
0.45
ClinPred
0.92
D
GERP RS
4.4
gMVP
0.11

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: chr16-82660712; API