Variant rs1471732983 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001797.4(CDH11):c.2383G>T(p.Asp795Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000688 in 1,452,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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: 32)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

CDH11
NM_001797.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.88

Variant links:

Genes affected

CDH11 (HGNC:1750): (cadherin 11) This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Expression of this particular cadherin in osteoblastic cell lines, and its upregulation during differentiation, suggests a specific function in bone development and maintenance. [provided by RefSeq, Jul 2008]

CDH11 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.32611668).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH11	NM_001797.4 link	c.2383G>T	p.Asp795Tyr	missense_variant	Exon 13 of 13	ENST00000268603.9	NP_001788.2	P55287-1
CDH11	NM_001330576.2 link	c.2005G>T	p.Asp669Tyr	missense_variant	Exon 12 of 12		NP_001317505.1	H3BUU9
CDH11	XM_047433486.1 link	c.2005G>T	p.Asp669Tyr	missense_variant	Exon 12 of 12		XP_047289442.1
CDH11	NM_001308392.2 link	c.*480G>T		3_prime_UTR_variant	Exon 14 of 14		NP_001295321.1	P55287-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CDH11	ENST00000268603.9 link	c.2383G>T	p.Asp795Tyr	missense_variant	Exon 13 of 13	1	NM_001797.4	ENSP00000268603.4	P55287-1
CDH11	ENST00000394156 link	c.*480G>T		3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000377711.3	P55287-2
CDH11	ENST00000566827.5 link	c.2005G>T	p.Asp669Tyr	missense_variant	Exon 12 of 12	2		ENSP00000457812.1	H3BUU9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.88e-7

AC:

AN:

1452648

Hom.:

Cov.:

AF XY:

0.00000139

AC XY:

AN XY:

720878

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:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000540

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Pathogenic

0.18

BayesDel_noAF

Uncertain

0.020

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.10

T;T

Eigen

Uncertain

0.58

Eigen_PC

Uncertain

0.64

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.88

D;D

M_CAP

Uncertain

0.087

MetaRNN

Benign

0.33

T;T

MetaSVM

Benign

-0.56

MutationAssessor

Benign

0.34

N;.

PrimateAI

Uncertain

0.72

PROVEAN

Benign

-1.5

N;N

REVEL

Benign

0.24

Sift

Uncertain

0.0010

D;D

Sift4G

Uncertain

0.0050

D;D

Polyphen

1.0

D;.

Vest4

0.46

MutPred

0.30

Gain of phosphorylation at D795 (P = 0.0108);.;

MVP

0.73

MPC

0.75

ClinPred

0.94

GERP RS

6.0

Varity_R

0.24

gMVP

0.69

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over