rs774357609
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_014176.4(UBE2T):āc.4C>Gā(p.Gln2Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,608 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000027 ( 0 hom. )
Consequence
UBE2T
NM_014176.4 missense
NM_014176.4 missense
Scores
3
5
6
Clinical Significance
Conservation
PhyloP100: 9.25
Genes affected
UBE2T (HGNC:25009): (ubiquitin conjugating enzyme E2 T) The protein encoded by this gene catalyzes the covalent attachment of ubiquitin to protein substrates. Defects in this gene have been associated with Fanconi anemia of complementation group T. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 1-202335751-G-C is Pathogenic according to our data. Variant chr1-202335751-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 199436.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-202335751-G-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE2T | NM_014176.4 | c.4C>G | p.Gln2Glu | missense_variant | 2/7 | ENST00000646651.1 | |
UBE2T | NM_001310326.2 | c.-91C>G | 5_prime_UTR_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE2T | ENST00000646651.1 | c.4C>G | p.Gln2Glu | missense_variant | 2/7 | NM_014176.4 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249478Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134906
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461608Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727112
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GnomAD4 genome ? Cov.: 32
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32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Fanconi anemia complementation group T Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 20, 2020 | - - |
Pathogenic, no assertion criteria provided | curation | Leiden Open Variation Database | Jul 19, 2015 | Curator: Arleen D. Auerbach. Submitter to LOVD: Johan den Dunnen. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 04, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
Polyphen
D;D
Vest4
0.91
MutPred
Loss of MoRF binding (P = 0.102);Loss of MoRF binding (P = 0.102);
MVP
0.75
MPC
0.68
ClinPred
D
GERP RS
Varity_R
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