NM_000294.3(PHKG2):c.502C>T (p.Arg168Ter) AND Glycogen storage disease IXc

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 25, 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:: RCV001958829.4

Allele description [Variation Report for NM_000294.3(PHKG2):c.502C>T (p.Arg168Ter)]

NM_000294.3(PHKG2):c.502C>T (p.Arg168Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_000294.3(PHKG2):c.502C>T (p.Arg168Ter)

HGVS:

NC_000016.10:g.30753503C>T
NG_016616.2:g.10205C>T
NM_000294.3:c.502C>TMANE SELECT
NM_001172432.2:c.502C>T
NP_000285.1:p.Arg168Ter
NP_001165903.1:p.Arg168Ter
NC_000016.9:g.30764824C>T
NG_016616.1:g.10205C>T

Protein change:

R168*

Links:

dbSNP: rs778952896

NCBI 1000 Genomes Browser:

rs778952896

Molecular consequence:

NM_000294.3:c.502C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001172432.2:c.502C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV002243319	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 25, 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

SCV002243319

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 25, 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, SCV002243319.3

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

Description

This sequence change creates a premature translational stop signal (p.Arg168*) 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 is present in population databases (rs778952896, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with clinical features of glycogen storage disease (PMID: 21646031). ClinVar contains an entry for this variant (Variation ID: 1459077). 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

Last Updated: Sep 29, 2024

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