17-3690125-C-A

Position:

• chr17-3690125-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002561.4(P2RX5):​c.559G>T​(p.Asp187Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: P2RX5 NM_002561.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

P2RX5 (HGNC:8536): (purinergic receptor P2X 5) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream gene, TAX1BP3 (Tax1 binding protein 3). [provided by RefSeq, Mar 2011]

P2RX5-TAX1BP3 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RX5	NM_002561.4	c.559G>T	p.Asp187Tyr	missense_variant	6/12	ENST00000225328.10
P2RX5-TAX1BP3	NR_037928.1	n.958G>T		non_coding_transcript_exon_variant	6/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RX5	ENST00000225328.10	c.559G>T	p.Asp187Tyr	missense_variant	6/12	1	NM_002561.4

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Uncertain	24
DANN	Uncertain	0.99
Eigen	Benign	-0.038
Eigen_PC	Benign	-0.063
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Uncertain	0.94	D;D;D;D;D;D
M_CAP	Benign	0.026	D
MetaRNN	Uncertain	0.65	D;D;D;D;D;D
MetaSVM	Benign	-0.86	T
MutationTaster	Benign	0.76	D;D;N;N;N;N;N
PrimateAI	Benign	0.33	T
Sift4G	Uncertain	0.0020	D;D;D;D;D;D
Polyphen		0.98, 0.99, 0.99	.;D;D;D;.;D
Vest4		0.57
MutPred		0.71		Gain of methylation at K183 (P = 0.0311);.;Gain of methylation at K183 (P = 0.0311);Gain of methylation at K183 (P = 0.0311);.;.;
MVP		0.28
MPC		0.63
ClinPred		0.99	D
GERP RS		-0.72
Varity_R		0.63
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-3593419; COSMIC: COSV56591255; COSMIC: COSV56591255;