rs606231226
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The ENST00000332007(DPP6):c.-340C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic,risk factor (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DPP6
ENST00000332007 5_prime_UTR
ENST00000332007 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.90
Genes affected
DPP6 (HGNC:3010): (dipeptidyl peptidase like 6) This gene encodes a single-pass type II membrane protein that is a member of the peptidase S9B family of serine proteases. This protein has no detectable protease activity, most likely due to the absence of the conserved serine residue normally present in the catalytic domain of serine proteases. However, it does bind specific voltage-gated potassium channels and alters their expression and biophysical properties. Variations in this gene may be associated with susceptibility to amyotrophic lateral sclerosis and with idiopathic ventricular fibrillation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 7-154305155-C-T is Pathogenic according to our data. Variant chr7-154305155-C-T is described in ClinVar as [Pathogenic, risk_factor]. Clinvar id is 16794.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr7-154305155-C-T is described in Lovd as [Likely_pathogenic]. Variant chr7-154305155-C-T is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPP6 | NM_130797.4 | c.244-141059C>T | intron_variant | ENST00000377770.8 | NP_570629.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPP6 | ENST00000377770.8 | c.244-141059C>T | intron_variant | 1 | NM_130797.4 | ENSP00000367001.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 609270Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0AN XY: 286652
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
AN:
609270
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8
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0
AN XY:
286652
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic; risk factor
Submissions summary: Pathogenic:2Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Ventricular fibrillation, paroxysmal familial, 2 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Apr 01, 2009 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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