Variant 2-46086342-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_005400.3(PRKCE):c.1572C>T(p.His524His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,599,336 control chromosomes in the GnomAD database, including 11,785 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.087 ( 1020 hom., cov: 32)

Exomes 𝑓: 0.10 ( 10765 hom. )

Consequence

PRKCE
NM_005400.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.12

Variant links:

Genes affected

PRKCE (HGNC:9401): (protein kinase C epsilon) Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and the second messenger diacylglycerol. PKC family members phosphorylate a wide variety of protein targets and are known to be involved in diverse cellular signaling pathways. PKC family members also serve as major receptors for phorbol esters, a class of tumor promoters. Each member of the PKC family has a specific expression profile and is believed to play a distinct role in cells. The protein encoded by this gene is one of the PKC family members. This kinase has been shown to be involved in many different cellular functions, such as neuron channel activation, apoptosis, cardioprotection from ischemia, heat shock response, as well as insulin exocytosis. Knockout studies in mice suggest that this kinase is important for lipopolysaccharide (LPS)-mediated signaling in activated macrophages and may also play a role in controlling anxiety-like behavior. [provided by RefSeq, Jul 2008]

PRKCE links:

PRKCE (HGNC:):

PRKCE links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP7

Synonymous conserved (PhyloP=2.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKCE	NM_005400.3 linkuse as main transcript	c.1572C>T	p.His524His	synonymous_variant	11/15	ENST00000306156.8	NP_005391.1	Q02156L7RTI5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PRKCE	ENST00000306156.8 linkuse as main transcript	c.1572C>T	p.His524His	synonymous_variant	11/15	1	NM_005400.3	ENSP00000306124.3	Q02156
PRKCE	ENST00000469753.5 linkuse as main transcript	n.659C>T		non_coding_transcript_exon_variant	2/4	3
PRKCE	ENST00000480633.1 linkuse as main transcript	n.338C>T		non_coding_transcript_exon_variant	2/4	2

Frequencies

GnomAD3 genomes

AF:

0.0869

AC:

13223

AN:

152118

Hom.:

1015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0216

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.0715

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.0809

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.0880

GnomAD3 exomes

AF:

0.138

AC:

32611

AN:

236692

Hom.:

3431

AF XY:

0.139

AC XY:

17983

AN XY:

129358

show subpopulations

Gnomad AFR exome

AF:

0.0202

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.0779

Gnomad EAS exome

AF:

0.426

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.0882

Gnomad NFE exome

AF:

0.0878

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.105

AC:

151763

AN:

1447100

Hom.:

10765

Cov.:

AF XY:

0.108

AC XY:

77661

AN XY:

720254

show subpopulations

Gnomad4 AFR exome

AF:

0.0149

Gnomad4 AMR exome

AF:

0.172

Gnomad4 ASJ exome

AF:

0.0754

Gnomad4 EAS exome

AF:

0.366

Gnomad4 SAS exome

AF:

0.209

Gnomad4 FIN exome

AF:

0.0962

Gnomad4 NFE exome

AF:

0.0882

Gnomad4 OTH exome

AF:

0.113

GnomAD4 genome

AF:

0.0869

AC:

13233

AN:

152236

Hom.:

1020

Cov.:

AF XY:

0.0912

AC XY:

6786

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0215

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.0715

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.0809

Gnomad4 NFE

AF:

0.0880

Gnomad4 OTH

AF:

0.0890

Alfa

AF:

0.0893

Hom.:

569

Bravo

AF:

0.0885

Asia WGS

AF:

0.282

AC:

979

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

8.1

DANN

Benign

0.72

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over