1-29258629-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_133178.4(PTPRU):c.330C>T(p.Asp110Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,614,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
PTPRU
NM_133178.4 synonymous
NM_133178.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.25
Genes affected
PTPRU (HGNC:9683): (protein tyrosine phosphatase receptor type U) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. This PTP was thought to play roles in cell-cell recognition and adhesion. Studies of the similar gene in mice suggested the role of this PTP in early neural development. The expression of this gene was reported to be regulated by phorbol myristate acetate (PMA) or calcium ionophore in Jurkat T lymphoma cells. Alternatively spliced transcript variants have been reported. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 1-29258629-C-T is Benign according to our data. Variant chr1-29258629-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3052506.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.25 with no splicing effect.
BS2
High AC in GnomAd4 at 33 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PTPRU | NM_133178.4 | c.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 30 | ENST00000373779.8 | NP_573439.2 | |
| PTPRU | NM_005704.5 | c.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 31 | NP_005695.3 | ||
| PTPRU | NM_133177.4 | c.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 31 | NP_573438.3 | ||
| PTPRU | NM_001195001.2 | c.330C>T | p.Asp110Asp | synonymous_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.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 30 | 1 | NM_133178.4 | ENSP00000362884.3 | ||
| PTPRU | ENST00000345512.7 | c.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 31 | 1 | ENSP00000334941.5 | |||
| PTPRU | ENST00000460170.2 | c.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 31 | 1 | ENSP00000432906.1 | |||
| PTPRU | ENST00000428026.6 | c.330C>T | p.Asp110Asp | synonymous_variant | Exon 3 of 30 | 1 | ENSP00000392332.2 |
Frequencies
GnomAD3 genomes 0.000217 AC: 33AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251372Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135876
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GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727248
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GnomAD4 genome 0.000217 AC: 33AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74500
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
PTPRU-related disorder Benign:1
Aug 15, 2019
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at