GeneBe

rs35264801

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_017859.4(UCKL1):​c.1568-17_1568-10delCCCCCCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000072 in 1,388,616 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: 0)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

UCKL1
NM_017859.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.810

Publications

0 publications found
Variant links:
Genes affected
UCKL1 (HGNC:15938): (uridine-cytidine kinase 1 like 1) The protein encoded by this gene is a uridine kinase. Uridine kinases catalyze the phosphorylation of uridine to uridine monophosphate. This protein has been shown to bind to Epstein-Barr nuclear antigen 3 as well as natural killer lytic-associated molecule. Ubiquitination of this protein is enhanced by the presence of natural killer lytic-associated molecule. In addition, protein levels decrease in the presence of natural killer lytic-associated molecule, suggesting that association with natural killer lytic-associated molecule results in ubiquitination and subsequent degradation of this protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017859.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
UCKL1
NM_017859.4
MANE Select
c.1568-17_1568-10delCCCCCCCC
intron
N/ANP_060329.2Q9NWZ5-1
UCKL1
NM_001353475.2
c.1571-17_1571-10delCCCCCCCC
intron
N/ANP_001340404.1
UCKL1
NM_001353476.2
c.1568-17_1568-10delCCCCCCCC
intron
N/ANP_001340405.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
UCKL1
ENST00000354216.11
TSL:1 MANE Select
c.1568-17_1568-10delCCCCCCCC
intron
N/AENSP00000346155.6Q9NWZ5-1
UCKL1
ENST00000883271.1
c.1598-17_1598-10delCCCCCCCC
intron
N/AENSP00000553330.1
UCKL1
ENST00000969434.1
c.1595-17_1595-10delCCCCCCCC
intron
N/AENSP00000639493.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.20e-7
AC:
1
AN:
1388616
Hom.:
0
AF XY:
0.00000144
AC XY:
1
AN XY:
692186
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32290
American (AMR)
AF:
0.00
AC:
0
AN:
42998
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24992
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38522
South Asian (SAS)
AF:
0.00
AC:
0
AN:
83458
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
45758
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5300
European-Non Finnish (NFE)
AF:
9.45e-7
AC:
1
AN:
1057682
Other (OTH)
AF:
0.00
AC:
0
AN:
57616
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs35264801; hg19: chr20-62571417; API