rs1553811652
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_004423.4(DVL3):c.1617del(p.Gln539HisfsTer129) 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 Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
DVL3
NM_004423.4 frameshift
NM_004423.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.40
Genes affected
DVL3 (HGNC:3087): (dishevelled segment polarity protein 3) This gene is a member of a multi-gene family which shares strong similarity with the Drosophila dishevelled gene, dsh. The Drosophila dishevelled gene encodes a cytoplasmic phosphoprotein that regulates cell proliferation. [provided by RefSeq, Jul 2008]
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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 3-184170123-AG-A is Pathogenic according to our data. Variant chr3-184170123-AG-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 488049.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-184170123-AG-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DVL3 | NM_004423.4 | c.1617del | p.Gln539HisfsTer129 | frameshift_variant | 14/15 | ENST00000313143.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DVL3 | ENST00000313143.9 | c.1617del | p.Gln539HisfsTer129 | frameshift_variant | 14/15 | 1 | NM_004423.4 | P1 | |
DVL3 | ENST00000431765.6 | c.1566del | p.Gln522HisfsTer129 | frameshift_variant | 14/15 | 5 | |||
DVL3 | ENST00000478247.1 | n.1617del | non_coding_transcript_exon_variant | 12/13 | 5 | ||||
DVL3 | ENST00000649847.1 | c.*547del | 3_prime_UTR_variant, NMD_transcript_variant | 9/10 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal dominant Robinow syndrome 2 Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Likely pathogenic, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Jun 01, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at