rs1445287184
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1PM2PP3PP5_Very_Strong
The NM_001145026.2(PTPRQ):c.6475C>T(p.Arg2159Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,550,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001145026.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRQ | NM_001145026.2 | c.6475C>T | p.Arg2159Ter | stop_gained | 42/45 | ENST00000644991.3 | |
LOC105369867 | XR_007063388.1 | n.130+36744G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRQ | ENST00000644991.3 | c.6475C>T | p.Arg2159Ter | stop_gained | 42/45 | NM_001145026.2 | P2 | ||
PTPRQ | ENST00000616559.4 | c.6574C>T | p.Arg2192Ter | stop_gained | 42/45 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 5AN: 156260Hom.: 0 AF XY: 0.0000242 AC XY: 2AN XY: 82782
GnomAD4 exome AF: 0.0000293 AC: 41AN: 1398606Hom.: 0 Cov.: 30 AF XY: 0.0000319 AC XY: 22AN XY: 689816
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74188
ClinVar
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 01, 2021 | Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 27535533, 23208854, 32860223) - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Feb 01, 2021 | - - |
Pes planus;C0030193:Pain;C0231686:Unsteady gait;C0728829:Pes cavus;C1384666:Hearing impairment;C1836843:Loss of ambulation;C1849134:Impaired vibration sensation in the lower limbs Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at