GeneBe

rs307941

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000479081.5(PRKCG):​c.-322-707T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PRKCG
ENST00000479081.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.838

Publications

6 publications found
Variant links:
Genes affected
PRKCG (HGNC:9402): (protein kinase C gamma) Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and 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 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 distinct roles in cells. The protein encoded by this gene is one of the PKC family members. This protein kinase is expressed solely in the brain and spinal cord and its localization is restricted to neurons. It has been demonstrated that several neuronal functions, including long term potentiation (LTP) and long term depression (LTD), specifically require this kinase. Knockout studies in mice also suggest that this kinase may be involved in neuropathic pain development. Defects in this protein have been associated with neurodegenerative disorder spinocerebellar ataxia-14 (SCA14). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
PRKCG Gene-Disease associations (from GenCC):
  • spinocerebellar ataxia type 14
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000479081.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRKCG
ENST00000474397.5
TSL:5
c.-323+10T>A
intron
N/AENSP00000471271.1
PRKCG
ENST00000479081.5
TSL:4
c.-322-707T>A
intron
N/AENSP00000471544.1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
3592
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2166
African (AFR)
AF:
0.00
AC:
0
AN:
16
American (AMR)
AF:
0.00
AC:
0
AN:
22
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
36
East Asian (EAS)
AF:
0.00
AC:
0
AN:
10
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1068
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
192
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
16
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
2062
Other (OTH)
AF:
0.00
AC:
0
AN:
170
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
6.3
DANN
Benign
0.50
PhyloP100
-0.84
PromoterAI
-0.016
Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs307941; hg19: chr19-54385104; API