3-122568841-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138287.3(DTX3L):c.752C>T(p.Pro251Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138287.3 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DTX3L | NM_138287.3 | c.752C>T | p.Pro251Leu | missense_variant | Exon 3 of 5 | ENST00000296161.9 | NP_612144.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 37AN: 249414Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 134984
GnomAD4 exome AF: 0.000211 AC: 308AN: 1461720Hom.: 0 Cov.: 31 AF XY: 0.000198 AC XY: 144AN XY: 727146
GnomAD4 genome AF: 0.000125 AC: 19AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.752C>T (p.P251L) alteration is located in exon 3 (coding exon 3) of the DTX3L gene. This alteration results from a C to T substitution at nucleotide position 752, causing the proline (P) at amino acid position 251 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