2-60960517-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_144709.4(PUS10):c.875G>A(p.Gly292Glu) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144709.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PUS10 | NM_144709.4 | c.875G>A | p.Gly292Glu | missense_variant, splice_region_variant | 11/18 | ENST00000316752.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PUS10 | ENST00000316752.11 | c.875G>A | p.Gly292Glu | missense_variant, splice_region_variant | 11/18 | 1 | NM_144709.4 | P1 | |
PUS10 | ENST00000602599.1 | n.3478G>A | splice_region_variant, non_coding_transcript_exon_variant | 9/16 | 1 | ||||
PUS10 | ENST00000407787.5 | c.875G>A | p.Gly292Glu | missense_variant, splice_region_variant | 11/18 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome Cov.: 28
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.875G>A (p.G292E) alteration is located in exon 11 (coding exon 10) of the PUS10 gene. This alteration results from a G to A substitution at nucleotide position 875, causing the glycine (G) at amino acid position 292 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.