NM_000294.3(PHKG2):c.334_337del (p.Lys112fs) AND Glycogen storage disease IXc

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jun 17, 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:: RCV002857514.6

Allele description [Variation Report for NM_000294.3(PHKG2):c.334_337del (p.Lys112fs)]

NM_000294.3(PHKG2):c.334_337del (p.Lys112fs)

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.334_337del (p.Lys112fs)

HGVS:

NC_000016.10:g.30753239_30753242del
NG_016616.2:g.9941_9944del
NM_000294.3:c.334_337delMANE SELECT
NM_001172432.2:c.334_337del
NP_000285.1:p.Lys112fs
NP_001165903.1:p.Lys112fs
NC_000016.9:g.30764558_30764561del
NC_000016.9:g.30764560_30764563del

Protein change:

K112fs

Links:

dbSNP: rs1567261757

Molecular consequence:

NM_000294.3:c.334_337del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172432.2:c.334_337del - 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
SCV003226314	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 30, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 8896567, 17689125, 21646031, 28492532
SCV005645749	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 17, 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

SCV003226314

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 30, 2022)

germline

clinical testing

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

SCV005645749

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 17, 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	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 (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003226314.4

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

Description

This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Lys112Glufs*29) 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). This variant has not been reported in the literature in individuals affected with PHKG2-related conditions. 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, SCV005645749.1

#	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

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