chr15-74837753-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001099436.4(ULK3):āc.1333A>Gā(p.Lys445Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,596,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K445R) has been classified as Likely benign.
Frequency
Consequence
NM_001099436.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ULK3 | NM_001099436.4 | c.1333A>G | p.Lys445Glu | missense_variant, splice_region_variant | 14/16 | ENST00000440863.7 | NP_001092906.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ULK3 | ENST00000440863.7 | c.1333A>G | p.Lys445Glu | missense_variant, splice_region_variant | 14/16 | 2 | NM_001099436.4 | ENSP00000400312 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000659 AC: 10AN: 151660Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000495 AC: 11AN: 222372Hom.: 0 AF XY: 0.0000332 AC XY: 4AN XY: 120390
GnomAD4 exome AF: 0.000150 AC: 217AN: 1444978Hom.: 0 Cov.: 40 AF XY: 0.000153 AC XY: 110AN XY: 717204
GnomAD4 genome AF: 0.0000659 AC: 10AN: 151660Hom.: 0 Cov.: 31 AF XY: 0.0000675 AC XY: 5AN XY: 74046
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.1333A>G (p.K445E) alteration is located in exon 14 (coding exon 14) of the ULK3 gene. This alteration results from a A to G substitution at nucleotide position 1333, causing the lysine (K) at amino acid position 445 to be replaced by a glutamic acid (E). 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