rs179363868
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM5
The NM_001099857.5(IKBKG):c.524G>A(p.Arg175Gln) variant causes a missense change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R175P) has been classified as Likely pathogenic.
Frequency
Genomes: 𝑓 0.0000098 ( 0 hom., 0 hem., cov: 19)
Exomes 𝑓: 0.0000030 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
IKBKG
NM_001099857.5 missense
NM_001099857.5 missense
Scores
1
10
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.74
Genes affected
IKBKG (HGNC:5961): (inhibitor of nuclear factor kappa B kinase regulatory subunit gamma) This gene encodes the regulatory subunit of the inhibitor of kappaB kinase (IKK) complex, which activates NF-kappaB resulting in activation of genes involved in inflammation, immunity, cell survival, and other pathways. Mutations in this gene result in incontinentia pigmenti, hypohidrotic ectodermal dysplasia, and several other types of immunodeficiencies. A pseudogene highly similar to this locus is located in an adjacent region of the X chromosome. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM5
Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IKBKG | NM_001099857.5 | c.524G>A | p.Arg175Gln | missense_variant | 5/10 | ENST00000594239.6 | NP_001093327.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IKBKG | ENST00000594239.6 | c.524G>A | p.Arg175Gln | missense_variant | 5/10 | 1 | NM_001099857.5 | ENSP00000471166.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 101770Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 28546 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000301 AC: 3AN: 997040Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 305558
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000982 AC: 1AN: 101791Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 28579
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;T;T;T;T;.;T;T
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;D;T;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
.;.;M;.;.;.;.;.;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.;N;.;.;.;.;.
REVEL
Uncertain
Sift
Benign
T;.;.;D;.;.;.;.;.
Sift4G
Benign
T;T;T;T;T;T;T;D;T
Polyphen
1.0, 1.0
.;D;D;.;.;.;.;.;D
Vest4
0.23, 0.22, 0.23, 0.21, 0.22
MutPred
Loss of MoRF binding (P = 0.0113);.;Loss of MoRF binding (P = 0.0113);.;Loss of MoRF binding (P = 0.0113);.;.;.;Loss of MoRF binding (P = 0.0113);
MVP
ClinPred
D
GERP RS
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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
Publications
No publications associated with this variant yet.