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10-6479019-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_006257.5(PRKCQ):c.1326G>A(p.Thr442=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00928 in 1,614,094 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0094 ( 85 hom. )

Consequence

PRKCQ
NM_006257.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.64
Variant links:
Genes affected
PRKCQ (HGNC:9410): (protein kinase C theta) 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. The protein encoded by this gene is one of the PKC family members. It is a calcium-independent and phospholipid-dependent protein kinase. This kinase is important for T-cell activation. It is required for the activation of the transcription factors NF-kappaB and AP-1, and may link the T cell receptor (TCR) signaling complex to the activation of the transcription factors. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-6479019-C-T is Benign according to our data. Variant chr10-6479019-C-T is described in ClinVar as [Benign]. Clinvar id is 784651.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.64 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 1247 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PRKCQNM_006257.5 linkuse as main transcriptc.1326G>A p.Thr442= synonymous_variant 12/18 ENST00000263125.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PRKCQENST00000263125.10 linkuse as main transcriptc.1326G>A p.Thr442= synonymous_variant 12/181 NM_006257.5 P1Q04759-1
PRKCQENST00000397176.6 linkuse as main transcriptc.1326G>A p.Thr442= synonymous_variant 12/175 Q04759-2
PRKCQENST00000539722.5 linkuse as main transcriptc.951G>A p.Thr317= synonymous_variant 11/172 Q04759-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00820
AC:
1247
AN:
152128
Hom.:
8
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00176
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00740
Gnomad ASJ
AF:
0.0144
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00270
Gnomad FIN
AF:
0.0175
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0118
Gnomad OTH
AF:
0.00574
GnomAD3 exomes
AF:
0.00883
AC:
2219
AN:
251316
Hom.:
17
AF XY:
0.00881
AC XY:
1197
AN XY:
135818
show subpopulations
Gnomad AFR exome
AF:
0.00154
Gnomad AMR exome
AF:
0.00416
Gnomad ASJ exome
AF:
0.0185
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00193
Gnomad FIN exome
AF:
0.0180
Gnomad NFE exome
AF:
0.0119
Gnomad OTH exome
AF:
0.0108
GnomAD4 exome
AF:
0.00939
AC:
13727
AN:
1461848
Hom.:
85
Cov.:
31
AF XY:
0.00930
AC XY:
6763
AN XY:
727220
show subpopulations
Gnomad4 AFR exome
AF:
0.00122
Gnomad4 AMR exome
AF:
0.00423
Gnomad4 ASJ exome
AF:
0.0174
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.00231
Gnomad4 FIN exome
AF:
0.0182
Gnomad4 NFE exome
AF:
0.0101
Gnomad4 OTH exome
AF:
0.0107
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00818
AC:
1246
AN:
152246
Hom.:
8
Cov.:
32
AF XY:
0.00814
AC XY:
606
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.00176
Gnomad4 AMR
AF:
0.00740
Gnomad4 ASJ
AF:
0.0144
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00249
Gnomad4 FIN
AF:
0.0175
Gnomad4 NFE
AF:
0.0118
Gnomad4 OTH
AF:
0.00568
Alfa
AF:
0.0106
Hom.:
6
Bravo
AF:
0.00676
Asia WGS
AF:
0.00318
AC:
12
AN:
3478
EpiCase
AF:
0.0106
EpiControl
AF:
0.00865

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeSep 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
1.2
Dann
Benign
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs17301189; hg19: chr10-6520981; API