chr5-111482885-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3PP5_Moderate

The NM_001744.6(CAMK4):​c.929T>C​(p.Met310Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CAMK4
NM_001744.6 missense

Scores

5
7
7

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 7.60
Variant links:
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 Uncertain_significance. Variant got 5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.825
PP5
Variant 5-111482885-T-C is Pathogenic according to our data. Variant chr5-111482885-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 2507053.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CAMK4NM_001744.6 linkuse as main transcriptc.929T>C p.Met310Thr missense_variant 10/11 ENST00000282356.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CAMK4ENST00000282356.9 linkuse as main transcriptc.929T>C p.Met310Thr missense_variant 10/111 NM_001744.6 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingGeneDxJun 29, 2023Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Uncertain
0.093
D
BayesDel_noAF
Benign
-0.10
CADD
Pathogenic
28
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.44
T;T
Eigen
Uncertain
0.66
Eigen_PC
Pathogenic
0.68
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.90
.;D
M_CAP
Benign
0.041
D
MetaRNN
Pathogenic
0.83
D;D
MetaSVM
Benign
-0.72
T
MutationAssessor
Benign
1.0
L;L
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.91
D
PROVEAN
Uncertain
-3.3
D;D
REVEL
Uncertain
0.29
Sift
Benign
0.044
D;D
Sift4G
Benign
0.087
T;T
Polyphen
1.0
D;D
Vest4
0.87
MutPred
0.49
Loss of stability (P = 0.0625);Loss of stability (P = 0.0625);
MVP
0.85
MPC
1.9
ClinPred
0.95
D
GERP RS
5.6
Varity_R
0.60
gMVP
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-110818583; API