5-180791818-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002406.4(MGAT1):c.1154G>A(p.Arg385Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000458 in 1,614,090 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 (★). Synonymous variant affecting the same amino acid position (i.e. R385R) has been classified as Likely benign.
Frequency
Consequence
NM_002406.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251328Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135868
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461888Hom.: 0 Cov.: 36 AF XY: 0.0000358 AC XY: 26AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1154G>A (p.R385Q) alteration is located in exon 3 (coding exon 1) of the MGAT1 gene. This alteration results from a G to A substitution at nucleotide position 1154, causing the arginine (R) at amino acid position 385 to be replaced by a glutamine (Q). 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