chr10-6497055-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006257.5(PRKCQ):c.640A>G(p.Ile214Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000693 in 1,613,110 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00039 ( 4 hom. )
Consequence
PRKCQ
NM_006257.5 missense
NM_006257.5 missense
Scores
14
Clinical Significance
Conservation
PhyloP100: -0.775
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 -9 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, PRKCQ
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0076305866).
BP6
?
Variant 10-6497055-T-C is Benign according to our data. Variant chr10-6497055-T-C is described in ClinVar as [Benign]. Clinvar id is 727330.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 551 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCQ | NM_006257.5 | c.640A>G | p.Ile214Val | missense_variant | 7/18 | ENST00000263125.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCQ | ENST00000263125.10 | c.640A>G | p.Ile214Val | missense_variant | 7/18 | 1 | NM_006257.5 | P1 | |
PRKCQ | ENST00000397176.6 | c.640A>G | p.Ile214Val | missense_variant | 7/17 | 5 | |||
PRKCQ | ENST00000539722.5 | c.265A>G | p.Ile89Val | missense_variant | 6/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00362 AC: 551AN: 152246Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00107 AC: 268AN: 251100Hom.: 1 AF XY: 0.000774 AC XY: 105AN XY: 135690
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GnomAD4 exome AF: 0.000388 AC: 567AN: 1460746Hom.: 4 Cov.: 32 AF XY: 0.000314 AC XY: 228AN XY: 726680
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GnomAD4 genome ? AF: 0.00362 AC: 551AN: 152364Hom.: 3 Cov.: 32 AF XY: 0.00327 AC XY: 244AN XY: 74510
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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 submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
Sift4G
Benign
T;T;T;T
Polyphen
0.0
.;B;B;.
Vest4
MVP
MPC
0.38
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at