1-29258624-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_133178.4(PTPRU):c.325C>T(p.Arg109Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,124 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_133178.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRU | NM_133178.4 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 30 | ENST00000373779.8 | NP_573439.2 | |
PTPRU | NM_005704.5 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 31 | NP_005695.3 | ||
PTPRU | NM_133177.4 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 31 | NP_573438.3 | ||
PTPRU | NM_001195001.2 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 30 | NP_001181930.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRU | ENST00000373779.8 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | ||
PTPRU | ENST00000345512.7 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 31 | 1 | ENSP00000334941.5 | |||
PTPRU | ENST00000460170.2 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 31 | 1 | ENSP00000432906.1 | |||
PTPRU | ENST00000428026.6 | c.325C>T | p.Arg109Trp | missense_variant | Exon 3 of 30 | 1 | ENSP00000392332.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251408Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135892
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727248
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.325C>T (p.R109W) alteration is located in exon 3 (coding exon 3) of the PTPRU gene. This alteration results from a C to T substitution at nucleotide position 325, causing the arginine (R) at amino acid position 109 to be replaced by a tryptophan (W). 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