rs35688758
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080418.3(DLGAP3):c.1721del(p.Gly574AlafsTer104) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
DLGAP3
NM_001080418.3 frameshift
NM_001080418.3 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.38
Genes affected
DLGAP3 (HGNC:30368): (DLG associated protein 3) Predicted to enable PDZ domain binding activity; molecular adaptor activity; and scaffold protein binding activity. Predicted to be involved in protein-containing complex assembly and regulation of postsynaptic neurotransmitter receptor activity. Predicted to be located in synapse. Predicted to be part of postsynaptic density. Predicted to be active in several cellular components, including cholinergic synapse; glutamatergic synapse; and neuromuscular junction. [provided by Alliance of Genome Resources, Apr 2022]
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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;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLGAP3 | NM_001080418.3 | c.1721del | p.Gly574AlafsTer104 | frameshift_variant | 7/12 | ENST00000373347.6 | |
DLGAP3 | XM_011541879.3 | c.1721del | p.Gly574AlafsTer104 | frameshift_variant | 8/13 | ||
DLGAP3 | XM_047426631.1 | c.1721del | p.Gly574AlafsTer104 | frameshift_variant | 7/12 | ||
DLGAP3 | XM_011541880.3 | c.230del | p.Gly77AlafsTer104 | frameshift_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLGAP3 | ENST00000373347.6 | c.1721del | p.Gly574AlafsTer104 | frameshift_variant | 7/12 | 5 | NM_001080418.3 | P1 | |
DLGAP3 | ENST00000235180.4 | c.1721del | p.Gly574AlafsTer104 | frameshift_variant | 5/10 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Not reported inComputational 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