NM_145262.4(GLYCTK):c.823G>A (p.Gly275Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 23, 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:: RCV001934997.8

Allele description [Variation Report for NM_145262.4(GLYCTK):c.823G>A (p.Gly275Ser)]

NM_145262.4(GLYCTK):c.823G>A (p.Gly275Ser)

Gene:

GLYCTK:glycerate kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.2

Genomic location:

Preferred name:

NM_145262.4(GLYCTK):c.823G>A (p.Gly275Ser)

HGVS:

NC_000003.12:g.52292377G>A
NG_023246.1:g.9558G>A
NM_001144951.2:c.647G>A
NM_145262.4:c.823G>AMANE SELECT
NP_001138423.1:p.Arg216Gln
NP_660305.2:p.Gly275Ser
NC_000003.11:g.52326393G>A
NR_026699.2:n.913G>A
NR_026700.2:n.495G>A
NR_026701.2:n.911G>A

Protein change:

G275S

Links:

dbSNP: rs769241961

NCBI 1000 Genomes Browser:

rs769241961

Molecular consequence:

NM_001144951.2:c.647G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_145262.4:c.823G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_026699.2:n.913G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_026700.2:n.495G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_026701.2:n.911G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Tssr37505 AND (alive[prop]) (0)
Gene
Methanobrevibacter sp. 87.7 contig37, whole genome shotgun sequence
Methanobrevibacter sp. 87.7 contig37, whole genome shotgun sequence
gi|1211946710|ref|NZ_MRCT01000037.1 |WGS:NZ_MRCT01|contig37

Nucleotide
Chain n, 60S ribosomal protein L41-A
Chain n, 60S ribosomal protein L41-A
gi|2509606120|pdb|8CAH|n

Protein
Chain B, 40S ribosomal protein S5
Chain B, 40S ribosomal protein S5
gi|2509606103|pdb|8CAH|B

Protein
Rattus norvegicus 342000077105768 genomic scaffold, whole genome shotgun sequenc...
Rattus norvegicus 342000077105768 genomic scaffold, whole genome shotgun sequence
gi|71679483|gb|CH474017.1||gnl|WGS: 342000077105768

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002172595	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 23, 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

SCV002172595

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 23, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002172595.4

#	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. 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 tolerated. ClinVar contains an entry for this variant (Variation ID: 1401070). This variant has not been reported in the literature in individuals affected with GLYCTK-related conditions. This variant is present in population databases (rs769241961, gnomAD 0.01%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 275 of the GLYCTK protein (p.Gly275Ser).

#	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: Sep 29, 2024

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