chr11-64757779-C-T

Variant names:

• chr11-64757779-C-T
• rs142234258
• NM_005609.4:c.660G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PP3_Moderate BS1_Supporting BS2_Supporting

The NM_005609.4(PYGM):​c.660G>A​(p.Gln220Gln) 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 NM_005609.4 splice_region, synonymous
• Scores: Splicing: ADA: 0.9997
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:12 B:2 O:1
• Conservation: PhyloP100: 5.02
• Publications: 4 publications found

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]

PYGM Gene-Disease associations (from GenCC):

• glycogen storage disease V

  Inheritance: AR, AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, Genomics England PanelApp

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00185 (282/152340) while in subpopulation SAS AF = 0.00891 (43/4826). AF 95% confidence interval is 0.0068. There are 0 homozygotes in GnomAd4. There are 114 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAdExome4 at 8 AR,AD 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 rank	MANE	Protein	UniProt
PYGM	NM_005609.4	c.660G>A	p.Gln220Gln	splice_region_variant, synonymous_variant	Exon 5 of 20	ENST00000164139.4	NP_005600.1
PYGM	NM_001164716.1	c.396G>A	p.Gln132Gln	splice_region_variant, synonymous_variant	Exon 3 of 18		NP_001158188.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYGM	ENST00000164139.4	c.660G>A	p.Gln220Gln	splice_region_variant, synonymous_variant	Exon 5 of 20	1	NM_005609.4	ENSP00000164139.3
PYGM	ENST00000377432.7	c.396G>A	p.Gln132Gln	splice_region_variant, synonymous_variant	Exon 3 of 18	2		ENSP00000366650.3

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

GnomAD2 exomes AF: 0.00209 AC: 524 AN: 251172 AF XY: 0.00244

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 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

African (AFR) AF: 0.000358 AC: 12 AN: 33480

American (AMR) AF: 0.00119 AC: 53 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.000650 AC: 17 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00655 AC: 565 AN: 86256

European-Finnish (FIN) AF: 0.0000562 AC: 3 AN: 53382

Middle Eastern (MID) AF: 0.00364 AC: 21 AN: 5768

European-Non Finnish (NFE) AF: 0.00267 AC: 2970 AN: 1111992

Other (OTH) AF: 0.00237 AC: 143 AN: 60396

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

African (AFR) AF: 0.000457 AC: 19 AN: 41584

American (AMR) AF: 0.00255 AC: 39 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00254 AC: 173 AN: 68026

Other (OTH) AF: 0.00236 AC: 5 AN: 2116

Alfa AF: 0.00222 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:12 Benign:2 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Glycogen storage disease, type V Pathogenic:2 Uncertain:5 Benign:1

Apr 14, 2020

Natera, Inc.

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Kids Neuroscience Centre, Sydney Children's Hospitals Network

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

May 14, 2018

CENTOGENE GmbH and LLC - Guiding Precision Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 05, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2023

Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 24, 2018

Counsyl

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Jun 10, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Uncertain:6

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PYGM: PP3, PS3:Supporting -

Jan 06, 2015

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 04, 2025

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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) -

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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not specified Uncertain:1 Benign:1

Aug 15, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

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PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Tip-toe gait Pathogenic:1

Dec 14, 2021

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

PYGM-related disorder Other:1

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GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant classified as Uncertain significance and reported on 08-23-2022 by GeneDx. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	25
DANN	Benign	0.92
PhyloP100		5.0
Mutation Taster		=5/95	disease causing

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

Other links and lift over

dbSNP: rs142234258; hg19: chr11-64525251;