rs3828323

Variant names:

• chr2-159951564-C-A
• NM_007366.5:c.3316G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-159951564-C-A
• chr2-159951564-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_007366.5(PLA2R1):​c.3316G>T​(p.Gly1106Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000216 in 1,389,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1106S) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: PLA2R1 NM_007366.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

Genes affected

PLA2R1 (HGNC:9042): (phospholipase A2 receptor 1) This gene represents a phospholipase A2 receptor. The encoded protein likely exists as both a transmembrane form and a soluble form. The transmembrane receptor may play a role in clearance of phospholipase A2, thereby inhibiting its action. Polymorphisms at this locus have been associated with susceptibility to idiopathic membranous nephropathy. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07138169).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2R1	NM_007366.5	c.3316G>T	p.Gly1106Cys	missense_variant	Exon 24 of 30	ENST00000283243.13	NP_031392.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2R1	ENST00000283243.13	c.3316G>T	p.Gly1106Cys	missense_variant	Exon 24 of 30	1	NM_007366.5	ENSP00000283243.7
PLA2R1	ENST00000392771.1	c.3316G>T	p.Gly1106Cys	missense_variant	Exon 24 of 27	1		ENSP00000376524.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000216 AC: 3 AN: 1389424 Hom.: 0 Cov.: 24 AF XY: 0.00000144 AC XY: 1 AN XY: 695560

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000287

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.1
DANN	Benign	0.71
DEOGEN2	Benign	0.034	T;.
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.059	N
LIST_S2	Benign	0.31	T;T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.071	T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.69	N;N
PrimateAI	Benign	0.20	T
PROVEAN	Benign	-1.3	N;N
REVEL	Benign	0.0090
Sift	Benign	0.10	T;T
Sift4G	Benign	0.20	T;T
Polyphen		0.15	B;B
Vest4		0.30
MutPred		0.43		Loss of disorder (P = 0.0035);Loss of disorder (P = 0.0035);
MVP		0.076
MPC		0.14
ClinPred		0.060	T
GERP RS		-3.0
Varity_R		0.067
gMVP		0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: chr2-160808075;