8-91071196-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_016023.5(OTUD6B):​c.141A>C​(p.Gln47His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

OTUD6B
NM_016023.5 missense

Scores

4
10
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.532
Variant links:
Genes affected
OTUD6B (HGNC:24281): (OTU deubiquitinase 6B) This gene encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Deubiquitinating enzymes are primarily involved in removing ubiquitin from proteins targeted for degradation. This protein may function as a negative regulator of the cell cycle in B cells. [provided by RefSeq, Nov 2013]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OTUD6BNM_016023.5 linkc.141A>C p.Gln47His missense_variant Exon 2 of 7 ENST00000404789.8 NP_057107.4 Q8N6M0-1A0A087X0W9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OTUD6BENST00000404789.8 linkc.141A>C p.Gln47His missense_variant Exon 2 of 7 1 NM_016023.5 ENSP00000384190.4 Q8N6M0-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.39
BayesDel_addAF
Pathogenic
0.18
D
BayesDel_noAF
Uncertain
0.020
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.15
T;T;T
Eigen
Benign
-0.14
Eigen_PC
Benign
-0.36
FATHMM_MKL
Benign
0.74
D
LIST_S2
Uncertain
0.93
D;.;D
M_CAP
Pathogenic
0.30
D
MetaRNN
Uncertain
0.73
D;D;D
MetaSVM
Pathogenic
0.87
D
MutationAssessor
Pathogenic
3.2
.;.;M
PrimateAI
Uncertain
0.70
T
PROVEAN
Uncertain
-3.6
.;D;.
REVEL
Uncertain
0.53
Sift
Uncertain
0.0030
.;D;.
Sift4G
Uncertain
0.0040
D;D;D
Polyphen
1.0
.;.;D
Vest4
0.70
MutPred
0.12
.;.;Loss of MoRF binding (P = 0.1029);
MVP
0.92
MPC
0.15
ClinPred
0.99
D
GERP RS
-3.8
Varity_R
0.37
gMVP
0.21

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11557571; hg19: chr8-92083424; API