1-85045215-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018298.11(MCOLN3):c.146C>G(p.Pro49Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,613,784 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P49S) has been classified 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCOLN3 | NM_018298.11 | c.146C>G | p.Pro49Arg | missense_variant | 2/13 | ENST00000370589.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCOLN3 | ENST00000370589.7 | c.146C>G | p.Pro49Arg | missense_variant | 2/13 | 1 | NM_018298.11 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251312Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135850
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727190
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 151994Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.146C>G (p.P49R) alteration is located in exon 2 (coding exon 1) of the MCOLN3 gene. This alteration results from a C to G substitution at nucleotide position 146, causing the proline (P) at amino acid position 49 to be replaced by an arginine (R). 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