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chr1-29260700-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_133178.4(PTPRU):​c.941A>G​(p.Asp314Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

PTPRU
NM_133178.4 missense

Scores

8
8
3

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.32
Variant links:
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 Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.813

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPRUNM_133178.4 linkuse as main transcriptc.941A>G p.Asp314Gly missense_variant 7/30 ENST00000373779.8
PTPRUNM_005704.5 linkuse as main transcriptc.941A>G p.Asp314Gly missense_variant 7/31
PTPRUNM_133177.4 linkuse as main transcriptc.941A>G p.Asp314Gly missense_variant 7/31
PTPRUNM_001195001.2 linkuse as main transcriptc.941A>G p.Asp314Gly missense_variant 7/30

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPRUENST00000373779.8 linkuse as main transcriptc.941A>G p.Asp314Gly missense_variant 7/301 NM_133178.4 A1Q92729-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 15, 2021The c.941A>G (p.D314G) alteration is located in exon 7 (coding exon 7) of the PTPRU gene. This alteration results from a A to G substitution at nucleotide position 941, causing the aspartic acid (D) at amino acid position 314 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.93
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
-0.020
CADD
Pathogenic
30
DANN
Uncertain
1.0
DEOGEN2
Benign
0.28
T;.;.;.
Eigen
Pathogenic
0.70
Eigen_PC
Uncertain
0.64
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Pathogenic
0.99
D;D;D;D
M_CAP
Uncertain
0.16
D
MetaRNN
Pathogenic
0.81
D;D;D;D
MetaSVM
Benign
-0.39
T
MutationAssessor
Pathogenic
3.0
M;M;M;M
MutationTaster
Benign
1.0
D;D;D;D;D;D
PrimateAI
Pathogenic
0.84
D
PROVEAN
Pathogenic
-5.6
D;D;D;D
REVEL
Uncertain
0.48
Sift
Uncertain
0.0010
D;D;D;D
Sift4G
Uncertain
0.0070
D;D;D;D
Polyphen
0.95
P;P;P;P
Vest4
0.85
MutPred
0.58
Loss of solvent accessibility (P = 0.0561);Loss of solvent accessibility (P = 0.0561);Loss of solvent accessibility (P = 0.0561);Loss of solvent accessibility (P = 0.0561);
MVP
0.48
MPC
1.9
ClinPred
1.0
D
GERP RS
5.2
Varity_R
0.79
gMVP
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-29587212; API