NM_004130.4(GYG1):c.491A>G (p.Gln164Arg) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 1, 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:: RCV003067282.2

Allele description

NM_004130.4(GYG1):c.491A>G (p.Gln164Arg)

Gene:

GYG1:glycogenin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q24

Genomic location:

Preferred name:

NM_004130.4(GYG1):c.491A>G (p.Gln164Arg)

HGVS:

NC_000003.12:g.149009285A>G
NG_027677.2:g.22747A>G
NM_001184720.2:c.491A>G
NM_001184721.2:c.491A>G
NM_004130.4:c.491A>GMANE SELECT
NP_001171649.1:p.Gln164Arg
NP_001171650.1:p.Gln164Arg
NP_004121.2:p.Gln164Arg
NC_000003.11:g.148727072A>G
NG_027677.1:g.22878A>G

Protein change:

Q164R

Molecular consequence:

NM_001184720.2:c.491A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001184721.2:c.491A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004130.4:c.491A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glycogen storage disease XV (GSD15)
Synonyms:: GLYCOGENIN DEFICIENCY; GSD XV
Identifiers:: MONDO: MONDO:0013291; MedGen: C3150754; Orphanet: 263297; OMIM: 613507

Name:: Polyglucosan body myopathy type 2
Identifiers:: MONDO: MONDO:0014526; MedGen: C4015452; Orphanet: 456369; OMIM: 616199

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003453748	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 1, 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

SCV003453748

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 1, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003453748.2

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

Description

This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 164 of the GYG1 protein (p.Gln164Arg). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with GYG1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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.

#	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 28, 2024

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