rs28730670

chr1-9717608-C-Achr1-9717608-C-Gchr1-9717608-C-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PS1 PM2 PP2 PP3_Moderate PP5_Moderate

The NM_005026.5(PIK3CD):c.1002C>A(p.Asn334Lys) 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. Variant has been reported in ClinVar as Likely pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Synonymous variant affecting the same amino acid position (i.e. N334N) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PIK3CD NM_005026.5 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: -0.927

Genes affected

PIK3CD (HGNC:8977): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta) Phosphoinositide 3-kinases (PI3Ks) phosphorylate inositol lipids and are involved in the immune response. The protein encoded by this gene is a class I PI3K found primarily in leukocytes. Like other class I PI3Ks (p110-alpha p110-beta, and p110-gamma), the encoded protein binds p85 adapter proteins and GTP-bound RAS. However, unlike the other class I PI3Ks, this protein phosphorylates itself, not p85 protein.[provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PS1: Transcript NM_005026.5 (PIK3CD) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 578525
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, PIK3CD
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.852
• PP5: Variant 1-9717608-C-A is Pathogenic according to our data. Variant chr1-9717608-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 132806.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIK3CD	NM_005026.5	c.1002C>A	p.Asn334Lys	missense_variant	8/24	ENST00000377346.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIK3CD	ENST00000377346.9	c.1002C>A	p.Asn334Lys	missense_variant	8/24	1	NM_005026.5	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.000136 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Immunodeficiency 14 Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Feb 24, 2023	This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 334 of the PIK3CD protein (p.Asn334Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of activated PIK3 delta syndrome (PMID: 24165795; Invitae; external communication). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 132806). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PIK3CD protein function. Experimental studies have shown that this missense change affects PIK3CD function (PMID: 24165795, 28167755). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.92
BayesDel_addAF	Benign	-0.076	T
BayesDel_noAF	Benign	-0.35
Cadd	Benign	13
Dann	Uncertain	0.98
Eigen	Benign	-0.49
Eigen_PC	Benign	-0.76
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Pathogenic	0.66	D
MetaRNN	Pathogenic	0.85	D;D;D;D;D
MetaSVM	Uncertain	0.12	D
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.69	T
PROVEAN	Pathogenic	-5.5	D;.;D;.;D
REVEL	Uncertain	0.44
Sift	Uncertain	0.0020	D;.;D;.;D
Sift4G	Uncertain	0.0040	D;D;D;D;D
Polyphen		1.0	D;.;D;D;.
Vest4		0.77
MutPred		0.40		Gain of methylation at N299 (P = 0.0143);Gain of methylation at N299 (P = 0.0143);.;Gain of methylation at N299 (P = 0.0143);Gain of methylation at N299 (P = 0.0143);
MVP		0.88
MPC		1.7
ClinPred		1.0	D
GERP RS		-7.4
Varity_R		0.93
gMVP		0.88

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: rs28730670; hg19: chr1-9777666; COSMIC: COSV63128871; COSMIC: COSV63128871;