rs77945315
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM1BP4_StrongBS1BS2
The NM_152221.3(CSNK1E):c.1223G>A(p.Ser408Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00112 in 1,606,320 control chromosomes in the GnomAD database, including 67 homozygotes. 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: 𝑓 0.00051 ( 5 hom., cov: 31)
Exomes 𝑓: 0.0012 ( 62 hom. )
Consequence
CSNK1E
NM_152221.3 missense
NM_152221.3 missense
Scores
1
5
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.71
Genes affected
CSNK1E (HGNC:2453): (casein kinase 1 epsilon) The protein encoded by this gene is a serine/threonine protein kinase and a member of the casein kinase I protein family, whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. The encoded protein is found in the cytoplasm as a monomer and can phosphorylate a variety of proteins, including itself. This protein has been shown to phosphorylate period, a circadian rhythm protein. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM1
?
In a modified_residue Phosphoserine (size 0) in uniprot entity KC1E_HUMAN
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008904189).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00118 (1723/1454306) while in subpopulation EAS AF= 0.0432 (1710/39584). AF 95% confidence interval is 0.0415. There are 62 homozygotes in gnomad4_exome. There are 840 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 77 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSNK1E | NM_152221.3 | c.1223G>A | p.Ser408Asn | missense_variant | 10/11 | ENST00000396832.6 | |
TPTEP2-CSNK1E | NM_001289912.2 | c.1223G>A | p.Ser408Asn | missense_variant | 14/15 | ||
CSNK1E | NM_001894.5 | c.1223G>A | p.Ser408Asn | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSNK1E | ENST00000396832.6 | c.1223G>A | p.Ser408Asn | missense_variant | 10/11 | 1 | NM_152221.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000507 AC: 77AN: 151896Hom.: 5 Cov.: 31
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GnomAD3 exomes AF: 0.000191 AC: 47AN: 246716Hom.: 0 AF XY: 0.000187 AC XY: 25AN XY: 133478
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GnomAD4 exome AF: 0.00118 AC: 1723AN: 1454306Hom.: 62 Cov.: 30 AF XY: 0.00116 AC XY: 840AN XY: 723596
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GnomAD4 genome ? AF: 0.000507 AC: 77AN: 152014Hom.: 5 Cov.: 31 AF XY: 0.000552 AC XY: 41AN XY: 74284
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;.
Vest4
MVP
MPC
1.0
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