18-41955344-A-T

Variant names:

• chr18-41955344-A-T
• rs371984369
• NM_002647.4:c.53A>T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_002647.4(PIK3C3):​c.53A>T​(p.Asn18Ile) 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 pathogenic 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. N18S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PIK3C3 NM_002647.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.90

Genes affected

PIK3C3 (HGNC:8974): (phosphatidylinositol 3-kinase catalytic subunit type 3) Enables 1-phosphatidylinositol-3-kinase activity. Involved in early endosome to late endosome transport and regulation of cytokinesis. Acts upstream of or within autophagy and protein lipidation. Located in autolysosome; late endosome; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.778

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIK3C3	NM_002647.4	c.53A>T	p.Asn18Ile	missense_variant	Exon 1 of 25	ENST00000262039.9	NP_002638.2
PIK3C3	NM_001308020.2	c.53A>T	p.Asn18Ile	missense_variant	Exon 1 of 24		NP_001294949.1
PIK3C3	XM_047437549.1	c.53A>T	p.Asn18Ile	missense_variant	Exon 1 of 22		XP_047293505.1
PIK3C3	XM_047437551.1	c.53A>T	p.Asn18Ile	missense_variant	Exon 1 of 14		XP_047293507.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIK3C3	ENST00000262039.9	c.53A>T	p.Asn18Ile	missense_variant	Exon 1 of 25	1	NM_002647.4	ENSP00000262039.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Uncertain	0.13
CADD	Uncertain	25
DANN	Benign	0.95
DEOGEN2	Pathogenic	0.81	D;.;T;.
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.58
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Uncertain	0.97	D;D;D;D
M_CAP	Pathogenic	0.34	D
MetaRNN	Pathogenic	0.78	D;D;D;D
MetaSVM	Uncertain	-0.19	T
MutationAssessor	Benign	2.0	M;.;.;.
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-4.9	D;.;D;.
REVEL	Uncertain	0.46
Sift	Benign	0.39	T;.;D;.
Sift4G	Benign	0.39	T;.;D;T
Polyphen		0.13	B;.;D;.
Vest4		0.82
MutPred		0.59		Loss of catalytic residue at N18 (P = 0.0409);Loss of catalytic residue at N18 (P = 0.0409);Loss of catalytic residue at N18 (P = 0.0409);Loss of catalytic residue at N18 (P = 0.0409);
MVP		0.85
MPC		0.33
ClinPred		0.98	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.78
gMVP		0.58

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

LitVar

Other links and lift over

dbSNP: rs371984369; hg19: chr18-39535309;