chr1-46194860-G-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
The NM_017739.4(POMGNT1):c.636C>T(p.Phe212Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_017739.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152036Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251122Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135864
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461830Hom.: 0 Cov.: 34 AF XY: 0.0000248 AC XY: 18AN XY: 727222
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74400
ClinVar
Submissions by phenotype
not provided Pathogenic:3
Reported previously in the homozygous and compound heterozygous state in patients with POMGNT1-related disorders (PMID: 17559086, 18330676, 23326386, 28424332, 32627857); This variant is demonstrated to destroy the canonical splice donor site and result in loss of function (PMID: 18330676); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 18330676, 22323514, 23326386, 19299310, 28424332, 28492532, 31589614, 35175440, 37342771, 38444904, 37597066, 17559086, 32627857) -
- -
- -
Muscle eye brain disease Pathogenic:2
- -
- -
Autosomal recessive limb-girdle muscular dystrophy Pathogenic:1
Variant summary: POMGNT1 c.636C>T alters a conserved nucleotide resulting in a synonymous change. 1/4 computational tools predicted weakening of the canonical 5' splice donor site. Multiple reports have demonstrated that this silent variant leads to exon 7 skipping, when analyzed at the RNA level (examples: Cummings_2017 and Oliveira_2008). The variant allele was found at a frequency of 4e-05 in 251122 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in POMGNT1 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive (4e-05 vs 0.00072), allowing no conclusion about variant significance. c.636C>T has been reported in the literature in individuals affected with muscular dystrophy and lissencephaly (examples: Bouchet_2007, Cummings_2017 and Oliveira_2008). These data indicate that the variant is very likely to be associated with disease. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Muscular dystrophy-dystroglycanopathy Pathogenic:1
The c.636C>T (p.Phe212=) variant in POMGNT1 has been reported in six individuals with muscular dystrophy-dystroglycanopathy (PMID 23326386, PMID 28424332, PMID 22323514, PMID 17559086, PMID 18330676) and has been identified in 0.01004% (2/19924) East Asian chromosomes in gnomAD (dbSNP ID rs190057175). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has been reported in ClinVar (Variation ID #265399) as pathogenic by GeneDx, Invitae, Counsyl, CeGaT Center for Human Genetics Tuebingen, Natera, Inc, and Perkin-Elmer Genomics. Of these six affected individuals, one was a homozygote (PMID: 18330676) and two were compound heterozygotes, one confirmed compound heterozygote who carried a pathogenic variant in confirmed trans (PMID: 28424332) and one compound heterozygote who carried a likely pathogenic variant in trans (PMID: 22323514), which increases the likelihood that the c.636C>T (p.Phe212=) variant is pathogenic. The variant was shown by RT-PCR analysis (PMID: 18330676, PMID: 17559086) and muscle RNAseq of patient tissue (PMID: 28424332) to alter splicing and lead to exon skipping of exon 7, frameshift, and premature truncation. Loss of function of the POMGNT1 gene is an established disease mechanism in autosomal recessive POMGNT1-associated muscular dystrophy-dystroglycanopathy. In summary, this variant meets criteria to be classified as pathogenic for POMGNT1-associated muscular dystrophy-dystroglycanopathy. ACMG/AMP Criteria applied: PM3_Strong, PM2_supporting, PS3_Strong (Richards 2015). -
Retinitis pigmentosa 76 Pathogenic:1
- -
Autosomal recessive limb-girdle muscular dystrophy type 2O Pathogenic:1
- -
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3;C3150417:Autosomal recessive limb-girdle muscular dystrophy type 2O;C3151519:Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3;C4310704:Retinitis pigmentosa 76 Pathogenic:1
- -
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3;C3150417:Autosomal recessive limb-girdle muscular dystrophy type 2O Pathogenic:1
This sequence change affects codon 212 of the POMGNT1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the POMGNT1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs190057175, gnomAD 0.006%). This variant has been observed in individual(s) with muscular dystrophy-dystroglycanopathy (PMID: 17559086, 18330676, 22323514, 23326386, 28424332). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 265399). Studies have shown that this variant results in skipping of exon 7, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 17559086, 18330676). For these reasons, this variant has been classified as Pathogenic. -
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 Pathogenic:1
- -
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3 Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at