19-48493921-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001388485.1(LMTK3):c.3865G>A(p.Glu1289Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000113 in 882,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388485.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMTK3 | NM_001388485.1 | c.3865G>A | p.Glu1289Lys | missense_variant | Exon 12 of 15 | ENST00000600059.6 | NP_001375414.1 | |
LMTK3 | NM_001080434.2 | c.3865G>A | p.Glu1289Lys | missense_variant | Exon 13 of 16 | NP_001073903.2 | ||
LMTK3 | XM_011526411.3 | c.3943G>A | p.Glu1315Lys | missense_variant | Exon 13 of 16 | XP_011524713.1 | ||
LMTK3 | XM_011526412.3 | c.3910G>A | p.Glu1304Lys | missense_variant | Exon 13 of 16 | XP_011524714.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000113 AC: 1AN: 882778Hom.: 0 Cov.: 30 AF XY: 0.00000241 AC XY: 1AN XY: 414730
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3952G>A (p.E1318K) alteration is located in exon 13 (coding exon 13) of the LMTK3 gene. This alteration results from a G to A substitution at nucleotide position 3952, causing the glutamic acid (E) at amino acid position 1318 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