rs78857302

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001145026.2(PTPRQ):​c.98C>A​(p.Thr33Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000216 in 1,388,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000022 ( 0 hom. )

Consequence

PTPRQ
NM_001145026.2 missense

Scores

1
5
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.11
Variant links:
Genes affected
PTPRQ (HGNC:9679): (protein tyrosine phosphatase receptor type Q) This locus encodes a member of the type III receptor-like protein-tyrosine phosphatase family. The encoded protein catalyzes the dephosphorylation of phosphotyrosine and phosphatidylinositol and plays roles in cellular proliferation and differentiation. Mutations at this locus have been linked to autosomal recessive deafness. [provided by RefSeq, Mar 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3305856).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTPRQNM_001145026.2 linkc.98C>A p.Thr33Asn missense_variant Exon 2 of 45 ENST00000644991.3 NP_001138498.1 A0A087WZU1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTPRQENST00000644991.3 linkc.98C>A p.Thr33Asn missense_variant Exon 2 of 45 NM_001145026.2 ENSP00000495607.1 A0A087WZU1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000130
AC:
2
AN:
153410
Hom.:
0
AF XY:
0.0000123
AC XY:
1
AN XY:
81408
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.000118
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000169
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000216
AC:
3
AN:
1388200
Hom.:
0
Cov.:
30
AF XY:
0.00000146
AC XY:
1
AN XY:
684888
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000404
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000187
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00000947
Hom.:
28
ExAC
AF:
0.0000462
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.093
T
BayesDel_noAF
Benign
-0.36
CADD
Benign
16
DANN
Benign
0.96
DEOGEN2
Benign
0.023
T;T;T;T;.;.
Eigen
Uncertain
0.31
Eigen_PC
Benign
0.19
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.73
T;T;T;T;.;T
M_CAP
Benign
0.025
D
MetaRNN
Benign
0.33
T;T;T;T;T;T
MetaSVM
Benign
-0.45
T
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-1.9
N;N;N;.;.;.
REVEL
Uncertain
0.32
Sift
Uncertain
0.0050
D;T;T;.;.;.
Sift4G
Pathogenic
0.0
D;D;D;D;D;.
Vest4
0.52, 0.72
MutPred
0.46
.;.;.;Gain of catalytic residue at S78 (P = 0);.;.;
MVP
0.26
ClinPred
0.54
D
GERP RS
4.9
gMVP
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs78857302; hg19: chr12-80838564; API