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NM_002637.4(PHKA1):c.389G>A (p.Trp130Ter) AND Glycogen storage disease IXd

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 11, 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:
RCV003867533.1

Allele description [Variation Report for NM_002637.4(PHKA1):c.389G>A (p.Trp130Ter)]

NM_002637.4(PHKA1):c.389G>A (p.Trp130Ter)

Genes:
PHKA1-AS1:PHKA1 antisense RNA 1 [Gene - HGNC]
PHKA1:phosphorylase kinase regulatory subunit alpha 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq13.1
Genomic location:
Preferred name:
NM_002637.4(PHKA1):c.389G>A (p.Trp130Ter)
HGVS:
  • NC_000023.11:g.72695773C>T
  • NG_016599.2:g.23409G>A
  • NM_001122670.2:c.389G>A
  • NM_001172436.2:c.389G>A
  • NM_002637.4:c.389G>AMANE SELECT
  • NP_001116142.1:p.Trp130Ter
  • NP_001165907.1:p.Trp130Ter
  • NP_002628.2:p.Trp130Ter
  • NC_000023.10:g.71915623C>T
Protein change:
W130*
Molecular consequence:
  • NM_001122670.2:c.389G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001172436.2:c.389G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_002637.4:c.389G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Glycogen storage disease IXd (GSD9D)
Synonyms:
GSD IXd
Identifiers:
MONDO: MONDO:0010362; MedGen: C1845151; Orphanet: 715; OMIM: 300559

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004674410Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 11, 2023) 		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

A splice junction mutation in the alpha(M) gene of phosphorylase kinase in a patient with myopathy.

Bruno C, Manfredi G, Andreu AL, Shanske S, Krishna S, Ilse WK, DiMauro S.

Biochem Biophys Res Commun. 1998 Aug 28;249(3):648-51.

PubMed [citation]
PMID:
9731190

Myopathy and phosphorylase kinase deficiency caused by a mutation in the PHKA1 gene.

Wuyts W, Reyniers E, Ceuterick C, Storm K, de Barsy T, Martin JJ.

Am J Med Genet A. 2005 Feb 15;133A(1):82-4.

PubMed [citation]
PMID:
15637709
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004674410.1

#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 affected with PHKA1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Trp130*) in the PHKA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHKA1 are known to be pathogenic (PMID: 9731190, 15637709).

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

Last Updated: Mar 5, 2024