chr12-131914363-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003565.4(ULK1):c.1259C>T(p.Pro420Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000931 in 1,610,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003565.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ULK1 | NM_003565.4 | c.1259C>T | p.Pro420Leu | missense_variant | 16/28 | ENST00000321867.6 | |
ULK1 | XM_011538798.4 | c.1259C>T | p.Pro420Leu | missense_variant | 16/28 | ||
ULK1 | XM_011538799.3 | c.1259C>T | p.Pro420Leu | missense_variant | 16/28 | ||
ULK1 | XR_007063134.1 | n.1639C>T | non_coding_transcript_exon_variant | 16/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ULK1 | ENST00000321867.6 | c.1259C>T | p.Pro420Leu | missense_variant | 16/28 | 1 | NM_003565.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152256Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247970Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134708
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1458708Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 725754
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152256Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 11, 2023 | The c.1259C>T (p.P420L) alteration is located in exon 16 (coding exon 16) of the ULK1 gene. This alteration results from a C to T substitution at nucleotide position 1259, causing the proline (P) at amino acid position 420 to be replaced by a leucine (L). 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