rs56282240
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_032237.5(POMK):c.882G>A(p.Gly294=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000891 in 1,614,136 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00093 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00089 ( 1 hom. )
Consequence
POMK
NM_032237.5 synonymous
NM_032237.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.138
Genes affected
POMK (HGNC:26267): (protein O-mannose kinase) This gene encodes a protein that may be involved in the presentation of the laminin-binding O-linked carbohydrate chain of alpha-dystroglycan (a-DG), which forms transmembrane linkages between the extracellular matrix and the exoskeleton. Some pathogens use this O-linked carbohydrate unit for host entry. Loss of function compound heterozygous mutations in this gene were found in a human patient affected by the Walker-Warburg syndrome (WWS) phenotype. Mice lacking this gene contain misplaced neurons (heterotopia) in some regions of the brain, possibly from defects in neuronal migration. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 8-43122706-G-A is Benign according to our data. Variant chr8-43122706-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 474197.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.138 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMK | NM_032237.5 | c.882G>A | p.Gly294= | synonymous_variant | 5/5 | ENST00000331373.10 | |
POMK | NM_001277971.2 | c.882G>A | p.Gly294= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMK | ENST00000331373.10 | c.882G>A | p.Gly294= | synonymous_variant | 5/5 | 2 | NM_032237.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000933 AC: 142AN: 152154Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00105 AC: 264AN: 251444Hom.: 0 AF XY: 0.000949 AC XY: 129AN XY: 135896
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GnomAD4 exome AF: 0.000887 AC: 1296AN: 1461864Hom.: 1 Cov.: 33 AF XY: 0.000862 AC XY: 627AN XY: 727230
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GnomAD4 genome ? AF: 0.000933 AC: 142AN: 152272Hom.: 1 Cov.: 33 AF XY: 0.00116 AC XY: 86AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | POMK: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2021 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12;C4015184:Limb-girdle muscular dystrophy due to POMK deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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