NM_145262.4(GLYCTK):c.1157T>G (p.Leu386Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 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:: RCV001990773.4

Allele description [Variation Report for NM_145262.4(GLYCTK):c.1157T>G (p.Leu386Arg)]

NM_145262.4(GLYCTK):c.1157T>G (p.Leu386Arg)

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.1157T>G (p.Leu386Arg)

HGVS:

NC_000003.12:g.52292711T>G
NG_023246.1:g.9892T>G
NM_001144951.2:c.*276T>G
NM_145262.4:c.1157T>GMANE SELECT
NP_660305.2:p.Leu386Arg
NC_000003.11:g.52326727T>G
NR_026699.2:n.1247T>G
NR_026701.2:n.1245T>G

Protein change:

L386R

Links:

dbSNP: rs2153221153

NCBI 1000 Genomes Browser:

rs2153221153

Molecular consequence:

NM_001144951.2:c.*276T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_145262.4:c.1157T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_026699.2:n.1247T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_026701.2:n.1245T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus golgi SNAP receptor complex member 2 (Gosr2), mRNA
Mus musculus golgi SNAP receptor complex member 2 (Gosr2), mRNA
gi|9789972|ref|NM_019650.1|

Nucleotide
OSBP(oxysterol binding protein)-related protein 3C [Arabidopsis thaliana]
OSBP(oxysterol binding protein)-related protein 3C [Arabidopsis thaliana]
gi|15238398|ref|NP_200750.1|

Protein
LisH and RanBPM domains containing protein [Arabidopsis thaliana]
LisH and RanBPM domains containing protein [Arabidopsis thaliana]
gi|42571941|ref|NP_974061.1|

Protein
Evaluation of Patients With Obesity - StatPearls
Evaluation of Patients With Obesity - StatPearls
XYLB [Canis lupus dingo]
XYLB [Canis lupus dingo]
Gene ID:112668755

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002261929	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 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

SCV002261929

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 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, SCV002261929.3

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

Description

ClinVar contains an entry for this variant (Variation ID: 1478772). 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 GLYCTK-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 386 of the GLYCTK protein (p.Leu386Arg).

#	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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