16-28538081-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012385.3(NUPR1):c.187G>A(p.Glu63Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000102 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012385.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUPR1 | NM_012385.3 | c.187G>A | p.Glu63Lys | missense_variant | Exon 2 of 3 | ENST00000324873.8 | NP_036517.1 | |
NUPR1 | NM_001042483.2 | c.241G>A | p.Glu81Lys | missense_variant | Exon 2 of 3 | NP_001035948.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251314Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135834
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.0000935 AC XY: 68AN XY: 727240
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.241G>A (p.E81K) alteration is located in exon 2 (coding exon 2) of the NUPR1 gene. This alteration results from a G to A substitution at nucleotide position 241, causing the glutamic acid (E) at amino acid position 81 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at