rs886039756
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_024818.6(UBA5):c.181C>T(p.Arg61Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
UBA5
NM_024818.6 stop_gained
NM_024818.6 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 1.50
Genes affected
UBA5 (HGNC:23230): (ubiquitin like modifier activating enzyme 5) This gene encodes a member of the E1-like ubiquitin-activating enzyme family. This protein activates ubiquitin-fold modifier 1, a ubiquitin-like post-translational modifier protein, via the formation of a high-energy thioester bond. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been identified on chromosome 1. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 3-132665842-C-T is Pathogenic according to our data. Variant chr3-132665842-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 265748.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-132665842-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBA5 | NM_024818.6 | c.181C>T | p.Arg61Ter | stop_gained | 2/12 | ENST00000356232.10 | |
NPHP3-ACAD11 | NR_037804.1 | n.3995+16072G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBA5 | ENST00000356232.10 | c.181C>T | p.Arg61Ter | stop_gained | 2/12 | 1 | NM_024818.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Mar 20, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 265748). This premature translational stop signal has been observed in individual(s) with UBA5-related conditions (PMID: 27545674). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg61*) in the UBA5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in UBA5 are known to be pathogenic (PMID: 27545674, 27545681). - |
Developmental and epileptic encephalopathy, 44 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 10, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A;A;A
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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