16-64948667-A-AC

Variant names:

• chr16-64948667-A-AC
• rs1315953324
• ENST00000394156.7:c.2014dupG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Moderate PM2

The NM_001308392.2(CDH11):​c.2014dupG​(p.Val672GlyfsTer186) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CDH11 NM_001308392.2 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.234

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0327 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH11	NM_001797.4	c.1895-569dupG		intron_variant	Intron 12 of 12	ENST00000268603.9	NP_001788.2
CDH11	NM_001308392.2	c.2014dupG	p.Val672GlyfsTer186	frameshift_variant	Exon 13 of 14		NP_001295321.1
CDH11	NM_001330576.2	c.1517-569dupG		intron_variant	Intron 11 of 11		NP_001317505.1
CDH11	XM_047433486.1	c.1517-569dupG		intron_variant	Intron 11 of 11		XP_047289442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH11	ENST00000394156.7	c.2014dupG	p.Val672GlyfsTer186	frameshift_variant	Exon 13 of 14	1		ENSP00000377711.3
CDH11	ENST00000268603.9	c.1895-569dupG		intron_variant	Intron 12 of 12	1	NM_001797.4	ENSP00000268603.4
CDH11	ENST00000566827.5	c.1517-569dupG		intron_variant	Intron 11 of 11	2		ENSP00000457812.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

CDH11-related disorder Uncertain:1

Mar 21, 2023

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CDH11 c.2014dupG variant is predicted to result in a frameshift and premature protein termination (p.Val672Glyfs*186). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Truncating variants in CDH11 have been reported in association with autosomal recessive Elsahy-Waters syndrome (see, for example, Castori et al. 2018. PubMed ID: 30194892; Harms et al. 2018. PubMed ID: 29271567). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

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: rs1315953324; hg19: chr16-64982570;