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NM_000292.3(PHKA2):c.2614G>T (p.Glu872Ter) AND Glycogen storage disease IXa1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 28, 2020
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:
RCV001972447.3

Allele description [Variation Report for NM_000292.3(PHKA2):c.2614G>T (p.Glu872Ter)]

NM_000292.3(PHKA2):c.2614G>T (p.Glu872Ter)

Gene:
PHKA2:phosphorylase kinase regulatory subunit alpha 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.13
Genomic location:
Preferred name:
NM_000292.3(PHKA2):c.2614G>T (p.Glu872Ter)
HGVS:
  • NC_000023.11:g.18906798C>A
  • NG_016622.1:g.82565G>T
  • NM_000292.3:c.2614G>TMANE SELECT
  • NP_000283.1:p.Glu872Ter
  • NC_000023.10:g.18924916C>A
Protein change:
E872*
Links:
dbSNP: rs2147855177
NCBI 1000 Genomes Browser:
rs2147855177
Molecular consequence:
  • NM_000292.3:c.2614G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Glycogen storage disease IXa1
Synonyms:
LIVER GLYCOGENOSIS, X-LINKED, TYPE I; GSD VIII; Glycogen storage disease 8; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010598; MedGen: C3694531; Orphanet: 264580; OMIM: 306000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002243134Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 28, 2020) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in the phosphorylase kinase gene PHKA2 are responsible for X-linked liver glycogen storage disease.

Hendrickx J, Coucke P, Dams E, Lee P, Odièvre M, Corbeel L, Fernandes JF, Willems PJ.

Hum Mol Genet. 1995 Jan;4(1):77-83.

PubMed [citation]
PMID:
7711737

Complete genomic structure and mutational spectrum of PHKA2 in patients with x-linked liver glycogenosis type I and II.

Hendrickx J, Lee P, Keating JP, Carton D, Sardharwalla IB, Tuchman M, Baussan C, Willems PJ.

Am J Hum Genet. 1999 Jun;64(6):1541-9.

PubMed [citation]
PMID:
10330341
PMCID:
PMC1377897
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002243134.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with PHKA2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu872*) in the PHKA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHKA2 are known to be pathogenic (PMID: 7711737, 10330341).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024