Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_017739.4(POMGNT1):c.440G>A(p.Arg147His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,876 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. R147C) has been classified as Uncertain significance.
POMGNT1 (HGNC:19139): (protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)) This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease and several congenital muscular dystrophies. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PP3
?
PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)
MetaRNN computational evidence supports a deleterious effect, 0.85
Uncertain significance, criteria provided, single submitter
clinical testing
Genetic Services Laboratory, University of Chicago
Sep 08, 2015
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Retinitis pigmentosa 76 Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Jul 22, 2021
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Autosomal recessive limb-girdle muscular dystrophy type 2O Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Jul 22, 2021
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Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3;C3150417:Autosomal recessive limb-girdle muscular dystrophy type 2O Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Invitae
Jul 14, 2022
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 147 of the POMGNT1 protein (p.Arg147His). This variant is present in population databases (rs776165339, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 436365). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POMGNT1 protein function. 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. -
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Jul 22, 2021
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3 Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Jul 22, 2021
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Muscle eye brain disease Uncertain:1
Uncertain significance, no assertion criteria provided