rs142234258

Positions:

• chr11-64757779-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting

The ENST00000164139.4(PYGM):​c.660G>A​(p.Gln220=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.00252 in 1,614,170 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0019 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0026 (8 hom.)
• Consequence: PYGM ENST00000164139.4 splice_region, synonymous
• Scores: Splicing: ADA: 0.9997
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:11 B:3
• Conservation: PhyloP100: 5.02

Genes affected

PYGM (HGNC:9726): (glycogen phosphorylase, muscle associated) This gene encodes a muscle enzyme involved in glycogenolysis. Highly similar enzymes encoded by different genes are found in liver and brain. Mutations in this gene are associated with McArdle disease (myophosphorylase deficiency), a glycogen storage disease of muscle. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 8 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PYGM	NM_005609.4	c.660G>A	p.Gln220=	splice_region_variant, synonymous_variant	5/20	ENST00000164139.4	NP_005600.1
PYGM	NM_001164716.1	c.396G>A	p.Gln132=	splice_region_variant, synonymous_variant	3/18		NP_001158188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PYGM	ENST00000164139.4	c.660G>A	p.Gln220=	splice_region_variant, synonymous_variant	5/20	1	NM_005609.4	ENSP00000164139	P1
PYGM	ENST00000377432.7	c.396G>A	p.Gln132=	splice_region_variant, synonymous_variant	3/18	2		ENSP00000366650

Frequencies

GnomAD3 genomes AF: 0.00185 AC: 282 AN: 152222 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000458

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00262

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00870

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00254

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.00209 AC: 524 AN: 251172 Hom.: 0 AF XY: 0.00244 AC XY: 331 AN XY: 135814

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.000781

Gnomad ASJ exome AF: 0.000894

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00611

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.00247

Gnomad OTH exome AF: 0.00261

GnomAD4 exome AF: 0.00259 AC: 3784 AN: 1461830 Hom.: 8 Cov.: 39 AF XY: 0.00277 AC XY: 2018 AN XY: 727220

Gnomad4 AFR exome AF: 0.000358

Gnomad4 AMR exome AF: 0.00119

Gnomad4 ASJ exome AF: 0.000650

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00655

Gnomad4 FIN exome AF: 0.0000562

Gnomad4 NFE exome AF: 0.00267

Gnomad4 OTH exome AF: 0.00237

GnomAD4 genome AF: 0.00185 AC: 282 AN: 152340 Hom.: 0 Cov.: 33 AF XY: 0.00153 AC XY: 114 AN XY: 74490

Gnomad4 AFR AF: 0.000457

Gnomad4 AMR AF: 0.00255

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00254

Gnomad4 OTH AF: 0.00236

Alfa AF: 0.00242 Hom.: 3

Bravo AF: 0.00185

Asia WGS AF: 0.00433 AC: 15 AN: 3478

EpiCase AF: 0.00333

EpiControl AF: 0.00290

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3 Uncertain:11 Benign:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Glycogen storage disease, type V Pathogenic:2 Uncertain:4 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Apr 14, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Kids Neuroscience Centre, Sydney Children's Hospitals Network	-	Detected two abnormal splicing events: (1) In-frame exon 5 skipping (r.529_660del). This event removes 44 amino acids from the glycogen phosphorylase domain of PYGM (p.(Met177_Gln220del)), of which 26 residues are conserved to Caenorhabditis elegans, (2) Exon 4 and exon 5 skipping (r.425_660del). This event induces a frameshift and encodes a premature termination codon (p.(Ala142Glyfs*32)). These transcripts are predicted to be targeted by nonsense-mediated decay (NMD). Any mis-spliced PYGM transcripts that escape NMD encode PYGM protein lacking 701 amino acids from the C-terminus, including 697 residues from the glycogen phosphorylase domain. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn	Feb 01, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	May 24, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	May 14, 2018	- -

not provided Uncertain:6

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 06, 2015	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2024	PYGM: PP3, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 01, 2024	Published functional studies indicate this variant leads to aberrant splicing, demonstrating a damaging effect (PMID: 34906502); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 25914343, 28967462, 34426522, 25987006, 34906502, 35628876) -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 15, 2024	Variant summary: PYGM c.660G>A (p.Gln220Gln) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. A recent publication reported experimental evidence that this variant affects mRNA splicing, demonstrating in-frame exon 5 skipping and out-of-frame exon 4-5 skipping, from whole blood derived RNA samples that were isolated from heterozygous carriers, however, the degree of mis-splicing (i.e. whether complete or partial) was not specified (Bournazos_2022). The variant allele was found at a frequency of 0.0025 in 1614170 control chromosomes, predominantly at a frequency of 0.0067 within the South Asian subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 1.9 fold of the estimated maximal expected allele frequency for a pathogenic variant in PYGM causing Glycogen Storage Disease, Type V phenotype (0.0035). c.660G>A has been reported in the literature in individuals affected with Glycogen Storage Disease, Type V (McArdle disease) (Zoccolella_2015, Inal-Gultekin_2017); however, in two of these reported patients who were from the same family, two co-occurring pathogenic variants were also present (although the phase was not specified), thus potentially explaining the phenotype (Inal-Gultekin_2017). Additionally, the variant was reported in a case of Limb-girdle muscular dystrophy in the homozygous state (Barbosa-Gouveia_2022) and a case of metabolic disease in the heterozgous state (Abolhassani_2024). These data do not allow any conclusion about variant significance. The following publications have been ascertained in the context of this evaluation (PMID: 38374194, 35628876, 34906502, 28967462, 25987006). ClinVar contains an entry for this variant (Variation ID: 197777). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Likely benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Tip-toe gait Pathogenic:1

Pathogenic, flagged submission

clinical testing

Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino

Dec 14, 2021

The Gln220= variant in PYGM does not lead to an amino acid exchange in the protein, but according to calculations by the prediction program varSEAK it could very likely lead to the generation of a new cryptic 5' donor splice site that would change the splice mechanism in intron 5. The variant was described in combination with another PYGM variant in a case report in a patient with symptoms of McArdle disease and multiple sclerosis [Zoccolella(2015) Neurol Sci 36(9):1721-3]. Toe Walking has various causes, ranging from idiopathic or habitual reasons to an underlying neuromuscular disease. The most observed form of toe walking is idiopathic toe walking (ITW) - a diagnosis of exclusion. ITW occurs in about 5% of children after their second birthday and is a common problem in pediatric orthopedics. In about 70% of these cases, there is spontaneous remission within six months of the onset of ITW. If the toe walk persists, one can assume the presence of a non-idiopathic form of toe walk (n-ITW). In n-ITW, the causes of the abnormal gait are neurological or myogenic. Differential diagnoses such as infantile cerebral palsy, muscular dystrophy, spinal amyotrophy and hereditary motor-sensory neuropathy as well as rare metabolic disorders of the musculature must be considered (Pomarino et al., 2018). In our clinical ITW consultation, we screen children with n-ITW for a genetic form of tiptoe gait using next generation sequencing for gene variants in 49 genes. These are genes in which gene variants can lead to neuromuscular diseases in which an association with toe-tapping gait has been reported or can be suspected due to patients’ clinical symptoms. To the best of our knowledge, this is the first study in which several patients with toe walking displayed heterozygosity for pathogenic or likely pathogenic PYGM mutations and mild symptoms of the metabolic muscle disease McArdle. The findings of our research are in line with recently published observations in heterozygous family members patients with McArdle disease. We should mention that some of the patients in our cohort harbored heterozygous variants in other genes of our gene panel. However, the numbers in this study were too small to workout any resulting combined genetic effects. It is concluded that genetic conditions can contribute to the development of toe walking. Apparently, even a slight genetic weakening of the muscles can lead to changes to the gait pattern. Future studies must show how the pathomechanism can be explained for the PYGM variants and whether there are new therapeutic approaches to be developed based on this research. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	25
DANN	Benign	0.92

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		0.65		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.65		Position offset: 16

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs142234258; hg19: chr11-64525251;