chr10-73821698-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001367534.1(CAMK2G):c.1233A>T(p.Glu411Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,459,444 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
CAMK2G
NM_001367534.1 missense
NM_001367534.1 missense
Scores
1
5
10
Clinical Significance
Conservation
PhyloP100: 1.04
Genes affected
CAMK2G (HGNC:1463): (calcium/calmodulin dependent protein kinase II gamma) The product of this gene is one of the four subunits of an enzyme which belongs to the serine/threonine protein kinase family, and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a gamma chain. Many alternatively spliced transcripts encoding different isoforms have been described but the full-length nature of all the variants has not been determined.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.2986291).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMK2G | NM_001367534.1 | c.1233A>T | p.Glu411Asp | missense_variant | 18/23 | ENST00000423381.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMK2G | ENST00000423381.6 | c.1233A>T | p.Glu411Asp | missense_variant | 18/23 | 5 | NM_001367534.1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 248084Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134016
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459444Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 725758
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
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32
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ExAC
?
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1
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.1137A>T (p.E379D) alteration is located in exon 16 (coding exon 16) of the CAMK2G gene. This alteration results from a A to T substitution at nucleotide position 1137, causing the glutamic acid (E) at amino acid position 379 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
A;D;D;D;D;D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
N;N;.;N;.;N;N;N
REVEL
Benign
Sift
Benign
T;T;.;T;.;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
B;B;.;.;B;.;B;.
Vest4
MutPred
0.28
.;.;.;.;Loss of methylation at K395 (P = 0.1359);.;Loss of methylation at K395 (P = 0.1359);.;
MVP
MPC
1.1
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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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