20-483965-T-C
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_ModerateBP6_Moderate
The NM_177559.3(CSNK2A1):āc.1172A>Gā(p.Gln391Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000027 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CSNK2A1
NM_177559.3 missense
NM_177559.3 missense
Scores
3
2
14
Clinical Significance
Conservation
PhyloP100: 5.28
Genes affected
CSNK2A1 (HGNC:2457): (casein kinase 2 alpha 1) Casein kinase II is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythm. The kinase exists as a tetramer and is composed of an alpha, an alpha-prime, and two beta subunits. The alpha subunits contain the catalytic activity while the beta subunits undergo autophosphorylation. The protein encoded by this gene represents the alpha subunit. Multiple transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Apr 2018]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CSNK2A1. . Gene score misZ 3.7123 (greater than the threshold 3.09). Trascript score misZ 5.3205 (greater than threshold 3.09). GenCC has associacion of gene with syndromic intellectual disability, Okur-Chung neurodevelopmental syndrome.
BP4
Computational evidence support a benign effect (MetaRNN=0.19654253).
BP6
Variant 20-483965-T-C is Benign according to our data. Variant chr20-483965-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1804402.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSNK2A1 | NM_177559.3 | c.1172A>G | p.Gln391Arg | missense_variant | 14/14 | ENST00000217244.9 | NP_808227.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSNK2A1 | ENST00000217244.9 | c.1172A>G | p.Gln391Arg | missense_variant | 14/14 | 1 | NM_177559.3 | ENSP00000217244.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248938Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134774
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000274 AC: 4AN: 1459614Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726118
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome Cov.: 32
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32
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3
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 27, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T;T;.;T;T;.;.;T;.;.;.;.;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;.;.;.;.;.;T;.;.;T;.;T;T;T;.;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;.;N;N;.;.;N;.;.;.;.;.;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
.;.;.;.;N;.;.;.;.;.;.;.;.;.;.;.
REVEL
Benign
Sift
Pathogenic
.;.;.;.;D;.;.;.;.;.;.;.;.;.;.;.
Sift4G
Pathogenic
.;.;.;.;D;.;.;.;.;.;.;.;.;.;.;.
Polyphen
B;B;B;.;B;B;.;.;B;.;.;.;.;.;B;B
Vest4
0.52
MutPred
Gain of stability (P = 0.0205);Gain of stability (P = 0.0205);Gain of stability (P = 0.0205);.;Gain of stability (P = 0.0205);Gain of stability (P = 0.0205);.;.;Gain of stability (P = 0.0205);.;.;.;.;.;Gain of stability (P = 0.0205);Gain of stability (P = 0.0205);
MVP
0.88
MPC
0.076
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
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