3-122566006-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138287.3(DTX3L):c.335C>T(p.Pro112Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DTX3L | NM_138287.3 | c.335C>T | p.Pro112Leu | missense_variant | Exon 2 of 5 | ENST00000296161.9 | NP_612144.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152112Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251466Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135908
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727248
GnomAD4 genome AF: 0.000151 AC: 23AN: 152112Hom.: 0 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.335C>T (p.P112L) alteration is located in exon 2 (coding exon 2) of the DTX3L gene. This alteration results from a C to T substitution at nucleotide position 335, causing the proline (P) at amino acid position 112 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