rs775024756
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001278512.2(AP3B2):c.199C>T(p.Arg67Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001278512.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP3B2 | NM_001278512.2 | c.199C>T | p.Arg67Ter | stop_gained | 3/27 | ENST00000535359.6 | |
CPEB1-AS1 | NR_046096.1 | n.1329-2788G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B2 | ENST00000535359.6 | c.199C>T | p.Arg67Ter | stop_gained | 3/27 | 1 | NM_001278512.2 | ||
CPEB1-AS1 | ENST00000560650.1 | n.1329-2788G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249226Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135210
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461694Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727128
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 48 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 19, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at