rs730880019
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The ENST00000395445.6(PCDH15):βc.5092_5094delβ(p.Glu1698del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000584 in 1,559,156 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β ).
Frequency
Genomes: π 0.000026 ( 0 hom., cov: 32)
Exomes π: 0.000062 ( 0 hom. )
Consequence
PCDH15
ENST00000395445.6 inframe_deletion
ENST00000395445.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.16
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]
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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;
BP3
Nonframeshift variant in repetitive region in ENST00000395445.6
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH15 | NM_001384140.1 | c.4671+1604_4671+1606del | intron_variant | ENST00000644397.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000644397.2 | c.4671+1604_4671+1606del | intron_variant | NM_001384140.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000718 AC: 12AN: 167216Hom.: 0 AF XY: 0.0000906 AC XY: 8AN XY: 88334
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GnomAD4 exome AF: 0.0000618 AC: 87AN: 1407002Hom.: 0 AF XY: 0.0000605 AC XY: 42AN XY: 694788
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 20, 2017 | The Glu1705del variant in PCDH15 has been previously reported by our laboratory in 1 individual with hearing loss; however, a variant affecting the remaining co py of PCDH15 was not identified. It has also been identified in 8/10848 East Asi an chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadin stitute.org; dbSNP rs730880019). This variant is an in-frame deletion of a singl e amino acid at position 1705 and is not predicted to alter the protein reading frame. In addition, the glutamine (Glu) residue at position 1705 is located in a region that is not well conserved across mammals or distant species suggesting that changes at this region may be tolerated; however, this information is insuf ficient to rule out pathogenicity. In summary, the clinical significance of this variant is uncertain. - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at