1-2050654-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_002744.6(PRKCZ):c.24G>A(p.Lys8Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000269 in 1,227,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
PRKCZ
NM_002744.6 synonymous
NM_002744.6 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.286
Genes affected
PRKCZ (HGNC:9412): (protein kinase C zeta) Protein kinase C (PKC) zeta is a member of the PKC family of serine/threonine kinases which are involved in a variety of cellular processes such as proliferation, differentiation and secretion. Unlike the classical PKC isoenzymes which are calcium-dependent, PKC zeta exhibits a kinase activity which is independent of calcium and diacylglycerol but not of phosphatidylserine. Furthermore, it is insensitive to typical PKC inhibitors and cannot be activated by phorbol ester. Unlike the classical PKC isoenzymes, it has only a single zinc finger module. These structural and biochemical properties indicate that the zeta subspecies is related to, but distinct from other isoenzymes of PKC. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 1-2050654-G-A is Benign according to our data. Variant chr1-2050654-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3771182.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.286 with no splicing effect.
BS2
High AC in GnomAdExome4 at 31 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKCZ | ENST00000378567.8 | c.24G>A | p.Lys8Lys | synonymous_variant | Exon 1 of 18 | 1 | NM_002744.6 | ENSP00000367830.3 | ||
PRKCZ | ENST00000468310.5 | c.24G>A | p.Lys8Lys | synonymous_variant | Exon 1 of 6 | 5 | ENSP00000424945.1 | |||
PRKCZ | ENST00000484419.1 | n.152G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000288 AC: 31AN: 1075016Hom.: 0 Cov.: 30 AF XY: 0.0000335 AC XY: 17AN XY: 507560
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74282
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Dec 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
PRKCZ: BP4, BP7 -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at