12-121274274-T-G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001270485.2(CAMKK2):c.253A>C(p.Thr85Pro) variant causes a missense 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. 15/22 in silico tools predict 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: 32)
Consequence
CAMKK2
NM_001270485.2 missense
NM_001270485.2 missense
Scores
1
18
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.550
Publications
40 publications found
Genes affected
CAMKK2 (HGNC:1470): (calcium/calmodulin dependent protein kinase kinase 2) The product of this gene belongs to the Serine/Threonine protein kinase family, and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. The major isoform of this gene plays a role in the calcium/calmodulin-dependent (CaM) kinase cascade by phosphorylating the downstream kinases CaMK1 and CaMK4. Protein products of this gene also phosphorylate AMP-activated protein kinase (AMPK). This gene has its strongest expression in the brain and influences signalling cascades involved with learning and memory, neuronal differentiation and migration, neurite outgrowth, and synapse formation. Alternative splicing results in multiple transcript variants encoding distinct isoforms. The identified isoforms differ in their ability to undergo autophosphorylation and to phosphorylate downstream kinases. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07403609).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CAMKK2 | NM_001270485.2 | c.253A>C | p.Thr85Pro | missense_variant | Exon 2 of 17 | ENST00000404169.8 | NP_001257414.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 50
GnomAD4 exome
Cov.:
50
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
.;.;.;.;T;.;T;T;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;.;.;T;.;T;T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
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;N;N;.;.
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;D;D;T;D;T;D;D;D;T;T;D
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T;T;.
Polyphen
B;B;B;B;B;B;B;B;B;B;.;.
Vest4
MutPred
Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);Gain of catalytic residue at L83 (P = 0.0041);
MVP
MPC
0.47
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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