3-142963146-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_198504.4(PAQR9):c.191G>A(p.Arg64Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,608,378 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 Uncertain significance (★).
Frequency
Consequence
NM_198504.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAQR9 | NM_198504.4 | c.191G>A | p.Arg64Gln | missense_variant | Exon 1 of 1 | ENST00000340634.6 | NP_940906.1 | |
PAQR9 | NM_001375300.1 | c.191G>A | p.Arg64Gln | missense_variant | Exon 2 of 4 | NP_001362229.1 | ||
PAQR9 | NM_001375301.1 | c.191G>A | p.Arg64Gln | missense_variant | Exon 2 of 4 | NP_001362230.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456172Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 723988
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.191G>A (p.R64Q) alteration is located in exon 1 (coding exon 1) of the PAQR9 gene. This alteration results from a G to A substitution at nucleotide position 191, causing the arginine (R) at amino acid position 64 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at