NM_002637.4(PHKA1):c.2101_2106del (p.Ser701_Leu702del) AND Glycogen storage disease IXd

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 4, 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:: RCV002944147.2

Allele description [Variation Report for NM_002637.4(PHKA1):c.2101_2106del (p.Ser701_Leu702del)]

NM_002637.4(PHKA1):c.2101_2106del (p.Ser701_Leu702del)

Gene:

PHKA1:phosphorylase kinase regulatory subunit alpha 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq13.1

Genomic location:

Preferred name:

NM_002637.4(PHKA1):c.2101_2106del (p.Ser701_Leu702del)

HGVS:

NC_000023.11:g.72620758_72620763del
NG_016599.2:g.98421_98426del
NM_001122670.2:c.2101_2106del
NM_001172436.2:c.1961-1456_1961-1451del
NM_002637.4:c.2101_2106delMANE SELECT
NP_001116142.1:p.Ser701_Leu702del
NP_002628.2:p.Ser701_Leu702del
NC_000023.10:g.71840606_71840611del
NC_000023.10:g.71840608_71840613del

Molecular consequence:

NM_001122670.2:c.2101_2106del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002637.4:c.2101_2106del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001172436.2:c.1961-1456_1961-1451del - intron variant - [Sequence Ontology: SO:0001627]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003285509	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 4, 2022)	germline	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

SCV003285509

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 4, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003285509.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.2101_2106del, results in the deletion of 2 amino acid(s) of the PHKA1 protein (p.Ser701_Leu702del), but otherwise preserves the integrity of the reading frame.

#	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: Feb 20, 2024

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