rs1555389881

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4

The NM_130839.5(UBE3A):​c.2162A>T​(p.Lys721Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

UBE3A
NM_130839.5 missense

Scores

2
7
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.08
Variant links:
Genes affected
UBE3A (HGNC:12496): (ubiquitin protein ligase E3A) This gene encodes an E3 ubiquitin-protein ligase, part of the ubiquitin protein degradation system. This imprinted gene is maternally expressed in brain and biallelically expressed in other tissues. Maternally inherited deletion of this gene causes Angelman Syndrome, characterized by severe motor and intellectual retardation, ataxia, hypotonia, epilepsy, absence of speech, and characteristic facies. The protein also interacts with the E6 protein of human papillomavirus types 16 and 18, resulting in ubiquitination and proteolysis of tumor protein p53. Alternative splicing of this gene results in three transcript variants encoding three isoforms with different N-termini. Additional transcript variants have been described, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
SNHG14 (HGNC:37462): (small nucleolar RNA host gene 14) This gene is located within the Prader-Willi critical region and produces a long, spliced paternally-imprinted RNA that initiates within a common upstream promoter region shared by the SNRPN (small nuclear ribonucleoprotein polypeptide N) and SNURF genes. This transcript serves as a host RNA for the small nucleolar RNA, C/D box 115 and 116 clusters. This RNA extends in antisense into the region of the ubiquitin protein ligase E3A gene (UBE3A), and is thought to regulate imprinted expression of UBE3A in the brain. This transcript undergoes extensive alternative splicing, and may initiate and terminate at multiple locations within this genomic region. The full-length structure of all splice forms is not determined. [provided by RefSeq, Mar 2017]

Genome browser will be placed here

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;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), UBE3A. . Trascript score misZ: 6.9443 (greater than threshold 3.09). The gene has 44 curated pathogenic missense variants (we use a threshold of 10). The gene has 8 curated benign missense variants. GenCC has associacion of the gene with Angelman syndrome.
BP4
Computational evidence support a benign effect (MetaRNN=0.38893163).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UBE3ANM_130839.5 linkc.2162A>T p.Lys721Ile missense_variant 10/13 ENST00000648336.2 NP_570854.1 Q05086-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UBE3AENST00000648336.2 linkc.2162A>T p.Lys721Ile missense_variant 10/13 NM_130839.5 ENSP00000497572.2 Q05086-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461214
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
726936
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

Angelman syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 23, 2018This sequence change replaces lysine with isoleucine at codon 701 of the UBE3A protein (p.Lys701Ile). The lysine residue is highly conserved and there is a moderate physicochemical difference between lysine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has been reported as maternally inherited in an individual referred for UBE3A gene testing, however the proband's mother and maternal grandmother were unaffected  (PMID: 25212744). Considering that UBE3A is maternally imprinted, the presence of maternal transmission (grandmother) to a clinically unaffected individual (mother) indicates that this variant is not a primary cause of disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.39
BayesDel_addAF
Uncertain
0.066
T
BayesDel_noAF
Benign
-0.14
CADD
Pathogenic
32
DANN
Uncertain
0.99
DEOGEN2
Benign
0.26
.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;T
Eigen
Uncertain
0.19
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.93
.;.;.;D;.;.;.;D;.;.;.;.;D;D;D;D
M_CAP
Benign
0.049
D
MetaRNN
Benign
0.39
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.67
T
MutationAssessor
Benign
1.6
.;.;.;.;.;.;.;.;.;L;.;.;.;.;L;.
PrimateAI
Uncertain
0.78
T
PROVEAN
Pathogenic
-4.6
.;.;.;.;D;.;.;.;.;.;.;D;D;.;D;.
REVEL
Benign
0.18
Sift
Benign
0.042
.;.;.;.;D;.;.;.;.;.;.;D;D;.;D;.
Sift4G
Benign
0.088
.;.;.;.;.;T;.;.;.;.;.;.;.;T;T;.
Polyphen
0.044, 0.27
.;B;.;.;.;B;.;B;.;B;.;.;.;.;B;.
Vest4
0.63, 0.63, 0.68, 0.64, 0.68, 0.68, 0.61
MutPred
0.60
.;.;.;.;.;.;.;.;.;Loss of MoRF binding (P = 0.0412);.;.;.;.;Loss of MoRF binding (P = 0.0412);.;
MVP
0.26
MPC
1.7
ClinPred
0.98
D
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.81
gMVP
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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: rs1555389881; hg19: chr15-25599793; API