rs142234258

chr11-64757779-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate

The NM_005609.4(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. 2/2 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: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 Uncertain_significance. Variant got 2 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.

Transcripts

RefSeq

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

Ensembl

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

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 pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn	Feb 01, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	May 14, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	May 24, 2018	- -

not provided Uncertain:6

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 02, 2023	Alters the last nucleotide of the exon and is predicted to destroy the splice donor site but the effect on protein function is unclear; This variant is associated with the following publications: (PMID: 25914343, 25987006, 28967462, 34426522, 34906502) -
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	Eurofins Ntd Llc (ga)	Jan 06, 2015	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2023	PYGM: PS3:Moderate, PP3 -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 18, 2023	Variant summary: Variant summary: PYGM c.660G>A (p.Gln220Gln) alters a conserved nucleotide located to the last nucleotide of exon 5, and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: four predict the variant weakens a 5' donor site. 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 0.0021 in 251172 control chromosomes, predominantly within the South Asian- (frequency 0.0061), Bulgarian- (0.0049) and Southern European (0.0038) subpopulations in the gnomAD database (v2.1 exomes dataset). The observed variant frequencies in these subpopulations are above the estimated maximal expected allele frequency for a pathogenic variant in PYGM causing Glycogen Storage Disease, Type V phenotype (0.0035), suggesting that the variant might be a benign polymorphism. The variant, c.660G>A, has been reported in the literature in at least three 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). These data do not provide clear conclusions about the variant significance. Eleven submitters have provided clinical-significance assessments for this variant in ClinVar after 2014 without evidence for independent evaluation, and classified the variant as pathogenic (n=1) / likely pathogenic (n=1), VUS (n=7), likely benign (n=1) / benign (n=1). 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, criteria provided, single submitter

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]. -

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;