8-11300059-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_015458.4(MTMR9):c.328C>A(p.Pro110Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,362 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. P110A) has been classified as Uncertain significance.
Frequency
Consequence
NM_015458.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTMR9 | NM_015458.4 | c.328C>A | p.Pro110Thr | missense_variant | Exon 3 of 10 | ENST00000221086.8 | NP_056273.2 | |
MTMR9 | XM_047422125.1 | c.328C>A | p.Pro110Thr | missense_variant | Exon 3 of 11 | XP_047278081.1 | ||
MTMR9 | XM_017013753.3 | c.328C>A | p.Pro110Thr | missense_variant | Exon 3 of 7 | XP_016869242.1 | ||
MTMR9 | XM_011543831.3 | c.-354C>A | upstream_gene_variant | XP_011542133.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251270Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135794
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461258Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726926
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.328C>A (p.P110T) alteration is located in exon 3 (coding exon 3) of the MTMR9 gene. This alteration results from a C to A substitution at nucleotide position 328, causing the proline (P) at amino acid position 110 to be replaced by a threonine (T). 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