NM_002863.5(PYGL):c.280C>T (p.Arg94Ter) AND Glycogen storage disease, type VI

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Feb 7, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000020502.14

Allele description [Variation Report for NM_002863.5(PYGL):c.280C>T (p.Arg94Ter)]

NM_002863.5(PYGL):c.280C>T (p.Arg94Ter)

Gene:

PYGL:glycogen phosphorylase L [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q22.1

Genomic location:

Preferred name:

NM_002863.5(PYGL):c.280C>T (p.Arg94Ter)

HGVS:

NC_000014.9:g.50937801G>A
NG_012796.1:g.11730C>T
NM_001163940.2:c.244-2616C>T
NM_002863.5:c.280C>TMANE SELECT
NP_002854.3:p.Arg94Ter
NC_000014.8:g.51404519G>A
NM_002863.3:c.280C>T
NM_002863.4:c.280C>T

Protein change:

R94*

Links:

dbSNP: rs113993973

Molecular consequence:

NM_001163940.2:c.244-2616C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_002863.5:c.280C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Glycogen storage disease, type VI (GSD6)
Synonyms:: GSD VI; HERS DISEASE; PHOSPHORYLASE DEFICIENCY GLYCOGEN-STORAGE DISEASE OF LIVER; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009294; MedGen: C0017925; Orphanet: 369; OMIM: 232700

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000040952	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (1) [See all records that cite this PMID]
SCV000932059	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 22, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 32268899, 9536091, 21646031, 28492532
SCV005629308	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 7, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000040952

GeneReviews

no classification provided

not provided

unknown

literature only

PubMed (1)
[See all records that cite this PMID]

SCV000932059

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 22, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV005629308

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 7, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glycogen Storage Disease Type VI..

Sallago JB, Weinstein DA.

2009 Apr 23 [updated 2026 Mar 5]. In: Adam MP, Bick S, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2026.

PubMed [citation]

PMID:: 20301760

Novel PYGL mutations in Chinese children leading to glycogen storage disease type VI: two case reports.

Luo X, Hu J, Gao X, Fan Y, Sun Y, Gu X, Qiu W.

BMC Med Genet. 2020 Apr 8;21(1):74. doi: 10.1186/s12881-020-01010-4.

PubMed [citation]

PMID:: 32268899
PMCID:: PMC7140494

See all PubMed Citations (6)

Details of each submission

From GeneReviews, SCV000040952.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	not provided	not provided	Assert pathogenicity		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000932059.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

ClinVar contains an entry for this variant (Variation ID: 21337). This premature translational stop signal has been observed in individual(s) with glycogen storage disease type VI (PMID: 32268899). This variant is present in population databases (rs113993973, gnomAD 0.005%). This sequence change creates a premature translational stop signal (p.Arg94*) in the PYGL gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PYGL are known to be pathogenic (PMID: 9536091, 21646031). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV005629308.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 12, 2026

ClinVar

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