rs778100619
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_033109.5(PNPT1):c.760C>T(p.Gln254Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q254Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_033109.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.760C>T | p.Gln254Ter | stop_gained | 9/28 | ENST00000447944.7 | |
PNPT1 | XM_005264629.3 | c.520C>T | p.Gln174Ter | stop_gained | 9/28 | ||
PNPT1 | XM_017005172.2 | c.520C>T | p.Gln174Ter | stop_gained | 8/27 | ||
PNPT1 | XM_047446161.1 | c.760C>T | p.Gln254Ter | stop_gained | 9/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPT1 | ENST00000447944.7 | c.760C>T | p.Gln254Ter | stop_gained | 9/28 | 1 | NM_033109.5 | P1 | |
PNPT1 | ENST00000415374.5 | c.760C>T | p.Gln254Ter | stop_gained, NMD_transcript_variant | 9/29 | 5 | |||
PNPT1 | ENST00000260604.8 | c.*315C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/27 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251036Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135694
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460936Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726786
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at