chr8-66835781-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001033578.3(SGK3):āc.544A>Gā(p.Lys182Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,210 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Consequence
SGK3
NM_001033578.3 missense
NM_001033578.3 missense
Scores
5
9
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.35
Genes affected
SGK3 (HGNC:10812): (serum/glucocorticoid regulated kinase family member 3) This gene is a member of the Ser/Thr protein kinase family and encodes a phosphoprotein with a PX (phox homology) domain. The protein phosphorylates several target proteins and has a role in neutral amino acid transport and activation of potassium and chloride channels. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.773
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGK3 | NM_001033578.3 | c.544A>G | p.Lys182Glu | missense_variant | 9/17 | ENST00000521198.7 | |
C8orf44-SGK3 | NM_001204173.2 | c.544A>G | p.Lys182Glu | missense_variant | 11/19 | ||
SGK3 | NM_013257.5 | c.544A>G | p.Lys182Glu | missense_variant | 9/17 | ||
SGK3 | NM_170709.3 | c.544A>G | p.Lys182Glu | missense_variant | 9/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGK3 | ENST00000521198.7 | c.544A>G | p.Lys182Glu | missense_variant | 9/17 | 1 | NM_001033578.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248896Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134756
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GnomAD4 exome Cov.: 30
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;.;.;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
L;L;L;L;.;L;L;.;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;N;D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;T;D;D;D;D
Sift4G
Uncertain
D;D;D;D;T;D;D;D;D
Polyphen
P;P;P;P;.;P;P;.;.
Vest4
MVP
MPC
ClinPred
D
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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