rs778907895
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032806.6(POMGNT2):c.332G>A(p.Arg111His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,046 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_032806.6 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 |
---|---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.332G>A | p.Arg111His | missense_variant | Exon 2 of 2 | ENST00000344697.3 | NP_116195.2 | |
POMGNT2 | XM_005265515.4 | c.332G>A | p.Arg111His | missense_variant | Exon 3 of 3 | XP_005265572.1 | ||
POMGNT2 | XM_011534163.3 | c.332G>A | p.Arg111His | missense_variant | Exon 3 of 3 | XP_011532465.1 | ||
POMGNT2 | XM_017007353.2 | c.332G>A | p.Arg111His | missense_variant | Exon 4 of 4 | XP_016862842.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251436Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135902
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461882Hom.: 0 Cov.: 37 AF XY: 0.0000110 AC XY: 8AN XY: 727242
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 540495). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 111 of the POMGNT2 protein (p.Arg111His). This variant is present in population databases (rs778907895, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with POMGNT2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at