1-29259521-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_133178.4(PTPRU):āc.632T>Cā(p.Met211Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000309 in 1,357,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_133178.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRU | NM_133178.4 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 30 | ENST00000373779.8 | NP_573439.2 | |
PTPRU | NM_005704.5 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 31 | NP_005695.3 | ||
PTPRU | NM_133177.4 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 31 | NP_573438.3 | ||
PTPRU | NM_001195001.2 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 30 | NP_001181930.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRU | ENST00000373779.8 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | ||
PTPRU | ENST00000345512.7 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 31 | 1 | ENSP00000334941.5 | |||
PTPRU | ENST00000460170.2 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 31 | 1 | ENSP00000432906.1 | |||
PTPRU | ENST00000428026.6 | c.632T>C | p.Met211Thr | missense_variant | Exon 5 of 30 | 1 | ENSP00000392332.2 |
Frequencies
GnomAD3 genomes AF: 0.00000731 AC: 1AN: 136748Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246418Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134132
GnomAD4 exome AF: 0.0000336 AC: 41AN: 1221104Hom.: 0 Cov.: 34 AF XY: 0.0000281 AC XY: 17AN XY: 604884
GnomAD4 genome AF: 0.00000731 AC: 1AN: 136748Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 65806
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.632T>C (p.M211T) alteration is located in exon 5 (coding exon 5) of the PTPRU gene. This alteration results from a T to C substitution at nucleotide position 632, causing the methionine (M) at amino acid position 211 to be replaced by a threonine (T). 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