rs267608259
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_015599.3(PGM3):c.1019_1021del(p.Glu340del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000000698 in 1,432,524 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
PGM3
NM_015599.3 inframe_deletion
NM_015599.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.93
Genes affected
PGM3 (HGNC:8907): (phosphoglucomutase 3) This gene encodes a member of the phosphohexose mutase family. The encoded protein mediates both glycogen formation and utilization by catalyzing the interconversion of glucose-1-phosphate and glucose-6-phosphate. A non-synonymous single nucleotide polymorphism in this gene may play a role in resistance to diabetic nephropathy and neuropathy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_015599.3. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 6-83178680-ACTT-A is Pathogenic according to our data. Variant chr6-83178680-ACTT-A is described in ClinVar as [Pathogenic]. Clinvar id is 156471.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM3 | NM_015599.3 | c.1019_1021del | p.Glu340del | inframe_deletion | 8/13 | ENST00000513973.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM3 | ENST00000513973.6 | c.1019_1021del | p.Glu340del | inframe_deletion | 8/13 | 1 | NM_015599.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.98e-7 AC: 1AN: 1432524Hom.: 0 AF XY: 0.00000140 AC XY: 1AN XY: 714730
GnomAD4 exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hyper-IgE syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | Centre of Chronic Immunodeficiency, Freiburg University | - | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at