chr5-111224521-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_001744.6(CAMK4):āc.38C>Gā(p.Ser13Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000569 in 1,459,100 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 (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.000057 ( 0 hom. )
Consequence
CAMK4
NM_001744.6 missense
NM_001744.6 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 4.42
Genes affected
CAMK4 (HGNC:1464): (calcium/calmodulin dependent protein kinase IV) The product of this gene belongs to the serine/threonine protein kinase family, and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. This enzyme is a multifunctional serine/threonine protein kinase with limited tissue distribution, that has been implicated in transcriptional regulation in lymphocytes, neurons and male germ cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM1
In a modified_residue Phosphoserine; by autocatalysis (size 0) in uniprot entity KCC4_HUMAN
BP4
Computational evidence support a benign effect (MetaRNN=0.22472626).
BS2
High AC in GnomAdExome4 at 83 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMK4 | NM_001744.6 | c.38C>G | p.Ser13Cys | missense_variant | 1/11 | ENST00000282356.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMK4 | ENST00000282356.9 | c.38C>G | p.Ser13Cys | missense_variant | 1/11 | 1 | NM_001744.6 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000286 AC: 7AN: 244478Hom.: 0 AF XY: 0.0000526 AC XY: 7AN XY: 133140
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GnomAD4 exome AF: 0.0000569 AC: 83AN: 1459100Hom.: 0 Cov.: 31 AF XY: 0.0000455 AC XY: 33AN XY: 725802
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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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 10, 2022 | The c.38C>G (p.S13C) alteration is located in exon 1 (coding exon 1) of the CAMK4 gene. This alteration results from a C to G substitution at nucleotide position 38, causing the serine (S) at amino acid position 13 to be replaced by a cysteine (C). 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
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;N;N
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;T;T
Sift4G
Uncertain
T;T;T
Polyphen
0.97
.;D;D
Vest4
0.41, 0.34
MutPred
Loss of glycosylation at S13 (P = 0.0223);Loss of glycosylation at S13 (P = 0.0223);Loss of glycosylation at S13 (P = 0.0223);
MVP
MPC
1.6
ClinPred
T
GERP RS
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