1-29258717-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_133178.4(PTPRU):c.418G>A(p.Gly140Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,609,554 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.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 30 | ENST00000373779.8 | NP_573439.2 | |
PTPRU | NM_005704.5 | c.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 31 | NP_005695.3 | ||
PTPRU | NM_133177.4 | c.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 31 | NP_573438.3 | ||
PTPRU | NM_001195001.2 | c.418G>A | p.Gly140Ser | 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.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | ||
PTPRU | ENST00000345512.7 | c.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 31 | 1 | ENSP00000334941.5 | |||
PTPRU | ENST00000460170.2 | c.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 31 | 1 | ENSP00000432906.1 | |||
PTPRU | ENST00000428026.6 | c.418G>A | p.Gly140Ser | missense_variant | Exon 3 of 30 | 1 | ENSP00000392332.2 |
Frequencies
GnomAD3 genomes AF: 0.000236 AC: 36AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000134 AC: 33AN: 246230Hom.: 0 AF XY: 0.000150 AC XY: 20AN XY: 133144
GnomAD4 exome AF: 0.000232 AC: 338AN: 1457208Hom.: 0 Cov.: 31 AF XY: 0.000237 AC XY: 172AN XY: 724452
GnomAD4 genome AF: 0.000230 AC: 35AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.418G>A (p.G140S) alteration is located in exon 3 (coding exon 3) of the PTPRU gene. This alteration results from a G to A substitution at nucleotide position 418, causing the glycine (G) at amino acid position 140 to be replaced by a serine (S). 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