rs144753553

Variant summary

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

The NM_024954.5(UBTD1):​c.73C>G​(p.Arg25Gly) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R25C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

UBTD1
NM_024954.5 missense, splice_region

Scores

5
8
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.10
Variant links:
Genes affected
UBTD1 (HGNC:25683): (ubiquitin domain containing 1) The degradation of many proteins is carried out by the ubiquitin pathway in which proteins are targeted for degradation by covalent conjugation of the polypeptide ubiquitin. This gene encodes a protein that belongs to the ubiquitin family of proteins. The encoded protein is thought to regulate E2 ubiquitin conjugating enzymes belonging to the UBE2D family. [provided by RefSeq, Mar 2014]

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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
UBTD1NM_024954.5 linkc.73C>G p.Arg25Gly missense_variant, splice_region_variant Exon 2 of 3 ENST00000370664.4 NP_079230.1 Q9HAC8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBTD1ENST00000370664.4 linkc.73C>G p.Arg25Gly missense_variant, splice_region_variant Exon 2 of 3 1 NM_024954.5 ENSP00000359698.3 Q9HAC8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.78
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Uncertain
0.13
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.21
T
Eigen
Uncertain
0.64
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.93
D
M_CAP
Benign
0.057
D
MetaRNN
Uncertain
0.61
D
MetaSVM
Benign
-0.64
T
MutationAssessor
Pathogenic
3.1
M
PrimateAI
Pathogenic
0.91
D
PROVEAN
Uncertain
-3.5
D
REVEL
Benign
0.29
Sift
Uncertain
0.0030
D
Sift4G
Benign
0.074
T
Polyphen
1.0
D
Vest4
0.81
MutPred
0.15
Loss of MoRF binding (P = 0.0845);
MVP
0.34
MPC
1.2
ClinPred
0.98
D
GERP RS
5.7
Varity_R
0.58
gMVP
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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: rs144753553; hg19: chr10-99327673; API