NM_002561.4:c.1060G>C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002561.4(P2RX5):c.1060G>C(p.Val354Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,610,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002561.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
P2RX5 | ENST00000225328.10 | c.1060G>C | p.Val354Leu | missense_variant | Exon 10 of 12 | 1 | NM_002561.4 | ENSP00000225328.5 | ||
P2RX5 | ENST00000697413.1 | c.1126G>C | p.Val376Leu | missense_variant | Exon 11 of 13 | ENSP00000513301.1 | ||||
P2RX5-TAX1BP3 | ENST00000550383.1 | n.1060G>C | non_coding_transcript_exon_variant | Exon 10 of 15 | 2 | ENSP00000455681.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251092Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135866
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457882Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 725520
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1060G>C (p.V354L) alteration is located in exon 10 (coding exon 10) of the P2RX5 gene. This alteration results from a G to C substitution at nucleotide position 1060, causing the valine (V) at amino acid position 354 to be replaced by a leucine (L). 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