1-29255340-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_133178.4(PTPRU):c.139G>A(p.Asp47Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,614,020 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.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 30 | ENST00000373779.8 | NP_573439.2 | |
PTPRU | NM_005704.5 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 31 | NP_005695.3 | ||
PTPRU | NM_133177.4 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 31 | NP_573438.3 | ||
PTPRU | NM_001195001.2 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 30 | NP_001181930.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRU | ENST00000373779.8 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | ||
PTPRU | ENST00000345512.7 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 31 | 1 | ENSP00000334941.5 | |||
PTPRU | ENST00000460170.2 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 31 | 1 | ENSP00000432906.1 | |||
PTPRU | ENST00000428026.6 | c.139G>A | p.Asp47Asn | missense_variant | Exon 2 of 30 | 1 | ENSP00000392332.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251370Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135894
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461838Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727230
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.139G>A (p.D47N) alteration is located in exon 2 (coding exon 2) of the PTPRU gene. This alteration results from a G to A substitution at nucleotide position 139, causing the aspartic acid (D) at amino acid position 47 to be replaced by an asparagine (N). 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