rs140516168
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033056.4(PCDH15):āc.1606G>Cā(p.Ala536Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000297 in 1,613,630 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Genomes: š 0.00017 ( 0 hom., cov: 32)
Exomes š: 0.000015 ( 0 hom. )
Consequence
PCDH15
NM_033056.4 missense
NM_033056.4 missense
Scores
2
6
8
Clinical Significance
Conservation
PhyloP100: 5.60
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 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21211696).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH15 | NM_033056.4 | c.1606G>C | p.Ala536Pro | missense_variant | 14/33 | ENST00000320301.11 | |
PCDH15 | NM_001384140.1 | c.1606G>C | p.Ala536Pro | missense_variant | 14/38 | ENST00000644397.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.1606G>C | p.Ala536Pro | missense_variant | 14/33 | 1 | NM_033056.4 | ||
PCDH15 | ENST00000644397.2 | c.1606G>C | p.Ala536Pro | missense_variant | 14/38 | NM_001384140.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152062Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251040Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135654
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461568Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727088
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GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74266
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 07, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 536 of the PCDH15 protein (p.Ala536Pro). This variant is present in population databases (rs140516168, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. ClinVar contains an entry for this variant (Variation ID: 229135). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The proline amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 17, 2017 | The p.Ala536Pro variant (rs140516168) has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the Genome Aggregation Database (gnomAD) with a frequency of 0.05 percent in the African population (identified on 13 out of 24,018 chromosomes) and has been reported to the ClinVar database as a variant of unknown significance (Variation ID: 229135). The alanine at position 536 is moderately conserved considering 12 species (Alamut v2.10) and computational analyses of the effects of the p.Ala536Pro variant on protein structure and function provide conflicting results (SIFT: tolerated, MutationTaster: disease causing, PolyPhen-2: probably damaging). Altogether, there is not enough evidence to classify the p.Ala536Pro variant with certainty. - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 06, 2015 | Variant classified as Uncertain Significance - Favor Benign. The p.Ala536Pro var iant in PCDH15 has not been previously reported in individuals with hearing loss , but has been identified in 0.1% (11/10404) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs140516168 ). The alanine (Ala) at position 536 is not conserved through species, with 2 ma mmals (dolphin and killer whale) having a proline (Pro) at this position, sugges ting that changes at this position may be tolerated. Additional computational pr ediction tools do not provide strong support for or against an impact to the pro tein. In summary, while the clinical significance of the p.Ala536Pro variant is uncertain, the conservation data suggest that it is more likely to be benign. - |
Usher syndrome type 1F Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 21, 2020 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.1606G>C (p.A536P) alteration is located in exon 14 (coding exon 13) of the PCDH15 gene. This alteration results from a G to C substitution at nucleotide position 1606, causing the alanine (A) at amino acid position 536 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;.;T;T;.;T;T;.;.;T;.;T;.;.;.;.;.;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
REVEL
Benign
Sift4G
Uncertain
D;.;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen
1.0, 0.95, 0.79, 1.0, 1.0
.;.;.;.;.;.;.;.;.;.;.;D;.;P;.;.;P;D;D;.;D;D;D
Vest4
MVP
MPC
0.038
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at