rs61755907
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001017995.3(SH3PXD2B):c.250C>T(p.Arg84Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,960 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 (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001017995.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3PXD2B | NM_001017995.3 | c.250C>T | p.Arg84Ter | stop_gained | 4/13 | ENST00000311601.6 | |
SH3PXD2B | NM_001308175.2 | c.250C>T | p.Arg84Ter | stop_gained | 4/13 | ||
SH3PXD2B | XM_017009351.2 | c.250C>T | p.Arg84Ter | stop_gained | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3PXD2B | ENST00000311601.6 | c.250C>T | p.Arg84Ter | stop_gained | 4/13 | 1 | NM_001017995.3 | P1 | |
SH3PXD2B | ENST00000519643.5 | c.250C>T | p.Arg84Ter | stop_gained | 4/13 | 1 | |||
SH3PXD2B | ENST00000636523.1 | c.208C>T | p.Arg70Ter | stop_gained | 4/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461762Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727186
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at