NM_000294.3(PHKG2):c.53_54del (p.Lys18fs) AND Glycogen storage disease IXc

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 15, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003628269.3

Allele description [Variation Report for NM_000294.3(PHKG2):c.53_54del (p.Lys18fs)]

NM_000294.3(PHKG2):c.53_54del (p.Lys18fs)

Gene:

PHKG2:phosphorylase kinase catalytic subunit gamma 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_000294.3(PHKG2):c.53_54del (p.Lys18fs)

HGVS:

NC_000016.10:g.30748873_30748874del
NG_016616.2:g.5575_5576del
NM_000294.3:c.53_54delMANE SELECT
NM_001172432.2:c.53_54del
NP_000285.1:p.Lys18fs
NP_001165903.1:p.Lys18fs
NC_000016.9:g.30760193_30760194del
NC_000016.9:g.30760194_30760195del

Protein change:

K18fs

Links:

dbSNP: rs2543449141

NCBI 1000 Genomes Browser:

rs2543449141

Molecular consequence:

NM_000294.3:c.53_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172432.2:c.53_54del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Glycogen storage disease IXc (GSD9C)
Synonyms:: GSD IXc
Identifiers:: MONDO: MONDO:0013091; MedGen: C2751643; Orphanet: 264580; OMIM: 613027

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004433550	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 15, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 8896567, 17689125, 21646031, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004433550

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 15, 2023)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Mutations in the testis/liver isoform of the phosphorylase kinase gamma subunit (PHKG2) cause autosomal liver glycogenosis in the gsd rat and in humans.

Maichele AJ, Burwinkel B, Maire I, Søvik O, Kilimann MW.

Nat Genet. 1996 Nov;14(3):337-40.

PubMed [citation]

PMID:: 8896567

Glycogen storage disease type IX: High variability in clinical phenotype.

Beauchamp NJ, Dalton A, Ramaswami U, Niinikoski H, Mention K, Kenny P, Kolho KL, Raiman J, Walter J, Treacy E, Tanner S, Sharrard M.

Mol Genet Metab. 2007 Sep-Oct;92(1-2):88-99. Epub 2007 Aug 3.

PubMed [citation]

PMID:: 17689125

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004433550.2

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PHKG2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys18Argfs*9) in the PHKG2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHKG2 are known to be pathogenic (PMID: 8896567, 17689125, 21646031).

#	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: May 16, 2025

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