NM_004130.4(GYG1):c.1009T>A (p.Ser337Thr) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 4, 2021
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:: RCV002024184.3

Allele description [Variation Report for NM_004130.4(GYG1):c.1009T>A (p.Ser337Thr)]

NM_004130.4(GYG1):c.1009T>A (p.Ser337Thr)

Gene:

GYG1:glycogenin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q24

Genomic location:

Preferred name:

NM_004130.4(GYG1):c.1009T>A (p.Ser337Thr)

HGVS:

NC_000003.12:g.149026889T>A
NG_027677.1:g.40482T>A
NM_001184720.2:c.958T>A
NM_001184721.2:c.738T>A
NM_004130.4:c.1009T>AMANE SELECT
NP_001171649.1:p.Ser320Thr
NP_001171650.1:p.Ile246=
NP_004121.2:p.Ser337Thr
NC_000003.11:g.148744676T>A

Protein change:

S320T

Links:

dbSNP: rs542123045

NCBI 1000 Genomes Browser:

rs542123045

Molecular consequence:

NM_001184720.2:c.958T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004130.4:c.1009T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001184721.2:c.738T>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV002308593	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 2021)	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

SCV002308593

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 2021)

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, SCV002308593.3

#	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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with GYG1-related conditions. This variant is present in population databases (rs542123045, ExAC 0.009%). This sequence change replaces serine with threonine at codon 337 of the GYG1 protein (p.Ser337Thr). The serine residue is moderately conserved and there is a small physicochemical difference between serine and threonine.

#	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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