rs281865414
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_001145026.2(PTPRQ):āc.715A>Gā(p.Arg239Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000776 in 399,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/8 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_001145026.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRQ | NM_001145026.2 | c.715A>G | p.Arg239Gly | missense_variant | 6/45 | ENST00000644991.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRQ | ENST00000644991.3 | c.715A>G | p.Arg239Gly | missense_variant | 6/45 | NM_001145026.2 | P2 | ||
PTPRQ | ENST00000616559.4 | c.841A>G | p.Arg281Gly | missense_variant | 7/45 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152184Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000931 AC: 23AN: 247154Hom.: 0 Cov.: 0 AF XY: 0.000104 AC XY: 13AN XY: 125234
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74360
ClinVar
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 84A Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 09, 2010 | - - |
not provided, no classification provided | literature only | ClinVar Staff, National Center for Biotechnology Information (NCBI) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at