NM_000292.3(PHKA2):c.3529C>T (p.Gln1177Ter) AND Glycogen storage disease IXa1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 15, 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:: RCV001329781.1

Allele description [Variation Report for NM_000292.3(PHKA2):c.3529C>T (p.Gln1177Ter)]

NM_000292.3(PHKA2):c.3529C>T (p.Gln1177Ter)

Genes:

PHKA2-AS1:PHKA2 antisense RNA 1 [Gene - HGNC]
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.3529C>T (p.Gln1177Ter)

HGVS:

NC_000023.11:g.18894212G>A
NG_016622.1:g.95151C>T
NM_000292.3:c.3529C>TMANE SELECT
NP_000283.1:p.Gln1177Ter
NC_000023.10:g.18912330G>A
NM_000292.2:c.3529C>T
NR_029379.1:n.533G>A

Protein change:

Q1177*

Links:

dbSNP: rs2047487518

NCBI 1000 Genomes Browser:

rs2047487518

Molecular consequence:

NR_029379.1:n.533G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000292.3:c.3529C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001521312	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 15, 2020)	de novo	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

SCV001521312

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 15, 2020)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Baylor Genetics, SCV001521312.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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