NM_003706.3:c.1160G>T

Variant names:

• chr19-48062095-C-A
• NM_003706.3:c.1160G>T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_003706.3(PLA2G4C):​c.1160G>T​(p.Gly387Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLA2G4C NM_003706.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

Genes affected

PLA2G4C (HGNC:9037): (phospholipase A2 group IVC) This gene encodes a protein which is a member of the phospholipase A2 enzyme family which hydrolyzes glycerophospholipids to produce free fatty acids and lysophospholipids, both of which serve as precursors in the production of signaling molecules. The encoded protein has been shown to be a calcium-independent and membrane bound enzyme. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]

PLA2G4C-AS1 (HGNC:51585): (PLA2G4C antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.89

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.1160G>T	p.Gly387Val	missense_variant	Exon 14 of 17	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1160G>T	p.Gly387Val	missense_variant	Exon 14 of 17	1	NM_003706.3	ENSP00000469473.1
PLA2G4C	ENST00000595161.5	c.224G>T	p.Gly75Val	missense_variant	Exon 3 of 5	3		ENSP00000469528.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Uncertain	0.098	D
BayesDel_noAF	Benign	-0.10
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.35	.;.;T;T
Eigen	Uncertain	0.27
Eigen_PC	Benign	0.089
FATHMM_MKL	Benign	0.29	N
LIST_S2	Benign	0.80	T;T;T;T
M_CAP	Benign	0.018	T
MetaRNN	Pathogenic	0.89	D;D;D;D
MetaSVM	Benign	-0.94	T
MutationAssessor	Pathogenic	3.2	.;M;M;.
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-7.3	.;D;.;.
REVEL	Benign	0.26
Sift	Pathogenic	0.0	.;D;.;.
Sift4G	Uncertain	0.0050	D;D;D;.
Polyphen		1.0	.;.;D;.
Vest4		0.50
MutPred		0.77		.;Loss of catalytic residue at L388 (P = 0.1111);Loss of catalytic residue at L388 (P = 0.1111);.;
MVP		0.54
MPC		0.55
ClinPred		0.99	D
GERP RS		1.6
Varity_R		0.61
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: chr19-48565352;