6-127513004-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001400265.1(MTCL3):c.1372G>A(p.Val458Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,532 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001400265.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTCL3 | NM_001400265.1 | c.1372G>A | p.Val458Met | missense_variant | Exon 4 of 7 | NP_001387194.1 | ||
SOGA3-KIAA0408 | NR_174482.1 | n.2217G>A | non_coding_transcript_exon_variant | Exon 4 of 13 | ||||
LOC107986642 | XR_001744337.2 | n.1171-1283C>T | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOGA3 | ENST00000525778.6 | c.1372G>A | p.Val458Met | missense_variant | Exon 4 of 7 | 5 | ENSP00000434570.1 | |||
ENSG00000255330 | ENST00000481848.6 | n.1372G>A | non_coding_transcript_exon_variant | Exon 4 of 12 | 5 | ENSP00000455908.1 | ||||
SOGA3 | ENST00000465909.3 | c.1372G>A | p.Val458Met | missense_variant | Exon 4 of 7 | 5 | ENSP00000435559.1 | |||
SOGA3 | ENST00000703793.1 | c.823G>A | p.Val275Met | missense_variant | Exon 3 of 5 | ENSP00000515479.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459532Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725850
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1372G>A (p.V458M) alteration is located in exon 4 (coding exon 3) of the SOGA3 gene. This alteration results from a G to A substitution at nucleotide position 1372, causing the valine (V) at amino acid position 458 to be replaced by a methionine (M). 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
Publications
No publications associated with this variant yet.