rs11553473
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_003345.5(UBE2I):c.73G>A(p.Val25Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,674 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
UBE2I
NM_003345.5 missense
NM_003345.5 missense
Scores
2
8
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 9.86
Genes affected
UBE2I (HGNC:12485): (ubiquitin conjugating enzyme E2 I) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Four alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
In a site Interaction with RANBP2 (size 0) in uniprot entity UBC9_HUMAN
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBE2I | NM_003345.5 | c.73G>A | p.Val25Met | missense_variant | 3/7 | ENST00000397514.8 | NP_003336.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBE2I | ENST00000397514.8 | c.73G>A | p.Val25Met | missense_variant | 3/7 | 1 | NM_003345.5 | ENSP00000380649.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461674Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727156
GnomAD4 exome
AF:
AC:
1
AN:
1461674
Hom.:
Cov.:
35
AF XY:
AC XY:
0
AN XY:
727156
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;.;T;T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;.;.;D;.;.;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;.;M;M;M;.;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
D;D;D;D;D;D;D;D;T;D
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T
Polyphen
D;D;D;D;.;D;D;D;.;D
Vest4
MutPred
Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);Gain of ubiquitination at K30 (P = 0.0579);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at