NM_018298.11:c.1460G>T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018298.11(MCOLN3):c.1460G>T(p.Ser487Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,612,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018298.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCOLN3 | ENST00000370589.7 | c.1460G>T | p.Ser487Ile | missense_variant | Exon 12 of 13 | 1 | NM_018298.11 | ENSP00000359621.1 | ||
MCOLN3 | ENST00000341115.8 | c.1292G>T | p.Ser431Ile | missense_variant | Exon 11 of 12 | 2 | ENSP00000342698.3 | |||
DNAI3 | ENST00000370596.5 | c.-15+21799C>A | intron_variant | Intron 1 of 21 | 5 | ENSP00000359628.1 | ||||
MCOLN3 | ENST00000474447.1 | n.1485G>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250794Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135556
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460564Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726636
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1460G>T (p.S487I) alteration is located in exon 12 (coding exon 11) of the MCOLN3 gene. This alteration results from a G to T substitution at nucleotide position 1460, causing the serine (S) at amino acid position 487 to be replaced by an isoleucine (I). 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