16-81786046-G-C

Variant names:

• chr16-81786046-G-C
• NM_002661.5:c.57G>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_002661.5(PLCG2):​c.57G>C​(p.Lys19Asn) 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 benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLCG2 NM_002661.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.07

Genes affected

PLCG2 (HGNC:9066): (phospholipase C gamma 2) The protein encoded by this gene is a transmembrane signaling enzyme that catalyzes the conversion of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate to 1D-myo-inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG) using calcium as a cofactor. IP3 and DAG are second messenger molecules important for transmitting signals from growth factor receptors and immune system receptors across the cell membrane. Mutations in this gene have been found in autoinflammation, antibody deficiency, and immune dysregulation syndrome and familial cold autoinflammatory syndrome 3. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.38202387).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCG2	NM_002661.5	c.57G>C	p.Lys19Asn	missense_variant	Exon 2 of 33	ENST00000564138.6	NP_002652.2
PLCG2	NM_001425749.1	c.57G>C	p.Lys19Asn	missense_variant	Exon 3 of 34		NP_001412678.1
PLCG2	NM_001425750.1	c.57G>C	p.Lys19Asn	missense_variant	Exon 2 of 33		NP_001412679.1
PLCG2	NM_001425751.1	c.57G>C	p.Lys19Asn	missense_variant	Exon 3 of 34		NP_001412680.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCG2	ENST00000564138.6	c.57G>C	p.Lys19Asn	missense_variant	Exon 2 of 33	1	NM_002661.5	ENSP00000482457.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Benign	-0.030	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.34	T;T;.
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.85	D;D;D
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.38	T;T;T
MetaSVM	Benign	-0.68	T
MutationAssessor	Benign	1.7	.;L;.
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-1.3	N;.;N
REVEL	Benign	0.15
Sift	Benign	0.31	T;.;T
Sift4G	Uncertain	0.039	D;T;T
Polyphen		0.99	.;D;.
Vest4		0.80, 0.75
MutPred		0.43		Loss of ubiquitination at K19 (P = 0.0174);Loss of ubiquitination at K19 (P = 0.0174);Loss of ubiquitination at K19 (P = 0.0174);
MVP		0.68
MPC		0.39
ClinPred		0.92	D
GERP RS		5.1
Varity_R		0.23
gMVP		0.68

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: chr16-81819651;