5-41313661-T-C

Variant names:

• chr5-41313661-T-C
• NM_001005473.3:c.922A>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001005473.3(PLCXD3):​c.922A>G​(p.Ile308Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLCXD3 NM_001005473.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.64
• Publications: 0 publications found

Genes affected

PLCXD3 (HGNC:31822): (phosphatidylinositol specific phospholipase C X domain containing 3) Predicted to enable phosphoric diester hydrolase activity. Predicted to be involved in lipid catabolic process and signal transduction. Predicted to be located in cytoplasm. Predicted to be active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3505394).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCXD3	NM_001005473.3	c.922A>G	p.Ile308Val	missense_variant	Exon 3 of 3	ENST00000377801.8	NP_001005473.1
PLCXD3	XM_017009438.3	c.706A>G	p.Ile236Val	missense_variant	Exon 3 of 3		XP_016864927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCXD3	ENST00000377801.8	c.922A>G	p.Ile308Val	missense_variant	Exon 3 of 3	1	NM_001005473.3	ENSP00000367032.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 07, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.922A>G (p.I308V) alteration is located in exon 3 (coding exon 3) of the PLCXD3 gene. This alteration results from a A to G substitution at nucleotide position 922, causing the isoleucine (I) at amino acid position 308 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Uncertain	0.060	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.043	T;T
Eigen	Uncertain	0.35
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.79	.;T
M_CAP	Benign	0.0063	T
MetaRNN	Benign	0.35	T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Uncertain	2.0	M;M
PhyloP100		7.6
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-0.75	N;N
REVEL	Benign	0.14
Sift	Uncertain	0.0090	D;D
Sift4G	Uncertain	0.024	D;D
Polyphen		0.52	P;P
Vest4		0.48
MutPred		0.54		Gain of ubiquitination at K309 (P = 0.0719);Gain of ubiquitination at K309 (P = 0.0719);
MVP		0.17
MPC		0.34
ClinPred		0.94	D
GERP RS		5.7
Varity_R		0.24
gMVP		0.41
Mutation Taster		=60/40	polymorphism

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

Other links and lift over

hg19: chr5-41313763;