rs1554956088

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The ENST00000320301.11(PCDH15):​c.2052C>A​(p.Tyr684Ter) variant causes a stop gained 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 Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

PCDH15
ENST00000320301.11 stop_gained

Scores

2
4
1

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 1.18
Variant links:
Genes affected
PCDH15 (HGNC:14674): (protocadherin related 15) This gene is a member of the cadherin superfamily. Family members encode integral membrane proteins that mediate calcium-dependent cell-cell adhesion. It plays an essential role in maintenance of normal retinal and cochlear function. Mutations in this gene result in hearing loss and Usher Syndrome Type IF (USH1F). Extensive alternative splicing resulting in multiple isoforms has been observed in the mouse ortholog. Similar alternatively spliced transcripts are inferred to occur in human, and additional variants are likely to occur. [provided by RefSeq, Dec 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 10-54079370-G-T is Pathogenic according to our data. Variant chr10-54079370-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 556543.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-54079370-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PCDH15NM_033056.4 linkuse as main transcriptc.2052C>A p.Tyr684Ter stop_gained 17/33 ENST00000320301.11 NP_149045.3
PCDH15NM_001384140.1 linkuse as main transcriptc.2052C>A p.Tyr684Ter stop_gained 17/38 ENST00000644397.2 NP_001371069.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCDH15ENST00000320301.11 linkuse as main transcriptc.2052C>A p.Tyr684Ter stop_gained 17/331 NM_033056.4 ENSP00000322604 Q96QU1-1
PCDH15ENST00000644397.2 linkuse as main transcriptc.2052C>A p.Tyr684Ter stop_gained 17/38 NM_001384140.1 ENSP00000495195

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Usher syndrome type 1F Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingCounsylFeb 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
38
DANN
Uncertain
1.0
Eigen
Uncertain
0.53
Eigen_PC
Uncertain
0.37
FATHMM_MKL
Uncertain
0.80
D
MutationTaster
Benign
1.0
A;A;A;A;A;A;A;A;A;A;A;A;A;D;D;D
Vest4
0.92
GERP RS
2.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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.

Other links and lift over

dbSNP: rs1554956088; hg19: chr10-55839130; API