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NM_002637.4(PHKA1):c.238-2A>T AND Glycogen storage disease IXd

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 17, 2022
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:
RCV002870683.2

Allele description [Variation Report for NM_002637.4(PHKA1):c.238-2A>T]

NM_002637.4(PHKA1):c.238-2A>T

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.238-2A>T
HGVS:
  • NC_000023.11:g.72705247T>A
  • NG_016599.2:g.13935A>T
  • NM_001122670.2:c.238-2A>T
  • NM_001172436.2:c.238-2A>T
  • NM_002637.4:c.238-2A>TMANE SELECT
  • NC_000023.10:g.71925096T>A
Molecular consequence:
  • NM_001122670.2:c.238-2A>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001172436.2:c.238-2A>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_002637.4:c.238-2A>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV003222087Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jul 17, 2022) 		germlineclinical testing

PubMed (4)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

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
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV003222087.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. This sequence change affects an acceptor splice site in intron 2 of the PHKA1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and 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: Feb 20, 2024