22-21023360-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005446.5(P2RX6):c.724C>T(p.Arg242Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R242H) has been classified as Likely benign.
Frequency
Consequence
NM_005446.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P2RX6 | ENST00000413302.7 | c.724C>T | p.Arg242Cys | missense_variant | Exon 7 of 12 | 1 | NM_005446.5 | ENSP00000416193.2 | ||
ENSG00000291240 | ENST00000706202.1 | n.1732+5976G>A | intron_variant | Intron 4 of 6 | ENSP00000516280.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251158Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135736
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461694Hom.: 0 Cov.: 35 AF XY: 0.0000261 AC XY: 19AN XY: 727130
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.724C>T (p.R242C) alteration is located in exon 7 (coding exon 7) of the P2RX6 gene. This alteration results from a C to T substitution at nucleotide position 724, causing the arginine (R) at amino acid position 242 to be replaced by a cysteine (C). 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