4-786591-G-T
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_006651.4(CPLX1):c.315C>A(p.Cys105*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_006651.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPLX1 | ENST00000304062.11 | c.315C>A | p.Cys105* | stop_gained | Exon 4 of 4 | 1 | NM_006651.4 | ENSP00000305613.6 | ||
CPLX1 | ENST00000505203.1 | c.252C>A | p.Cys84* | stop_gained | Exon 5 of 5 | 2 | ENSP00000425960.1 | |||
CPLX1 | ENST00000504062.1 | c.270C>A | p.Cys90* | stop_gained | Exon 3 of 3 | 3 | ENSP00000421947.1 | |||
CPLX1 | ENST00000506404.1 | n.368C>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 36
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 63 Pathogenic:3
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This variant is interpreted as Likely Pathogenic, for Epileptic encephalopathy, early infantile, 63, autosomal recessive. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PVS1-Strong => PVS1 downgraded in strength to Strong (https://www.ncbi.nlm.nih.gov/pubmed/28422131). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at