chr12-80444787-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001145026.2(PTPRQ):āc.101T>Gā(p.Ile34Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000195 in 1,540,150 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
PTPRQ
NM_001145026.2 missense
NM_001145026.2 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 2.42
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRQ | NM_001145026.2 | c.101T>G | p.Ile34Ser | missense_variant | 2/45 | ENST00000644991.3 | NP_001138498.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRQ | ENST00000644991.3 | c.101T>G | p.Ile34Ser | missense_variant | 2/45 | NM_001145026.2 | ENSP00000495607 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151844Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000144 AC: 2AN: 1388306Hom.: 0 Cov.: 30 AF XY: 0.00000146 AC XY: 1AN XY: 684926
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151844Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74176
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 12, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T;T;.;T
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;.;.;.
REVEL
Benign
Sift
Benign
T;T;T;.;.;.
Sift4G
Uncertain
D;D;D;D;D;.
Vest4
0.25, 0.34
MutPred
0.65
.;.;.;Gain of catalytic residue at S78 (P = 5e-04);.;.;
MVP
ClinPred
T
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gMVP
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at