NM_005476.7(GNE):c.101C>G (p.Thr34Ser) AND multiple conditions

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 18, 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:: RCV003019042.2

Allele description

NM_005476.7(GNE):c.101C>G (p.Thr34Ser)

Gene:

GNE:glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_005476.7(GNE):c.101C>G (p.Thr34Ser)

HGVS:

NC_000009.12:g.36249255G>C
NG_008246.1:g.32790C>G
NM_001128227.3:c.194C>G
NM_001190383.3:c.101C>G
NM_001190384.3:c.-13-2773C>G
NM_001190388.2:c.-13-2773C>G
NM_001374797.1:c.101C>G
NM_001374798.1:c.-13-2773C>G
NM_005476.7:c.101C>GMANE SELECT
NP_001121699.1:p.Thr65Ser
NP_001177312.1:p.Thr34Ser
NP_001361726.1:p.Thr34Ser
NP_005467.1:p.Thr34Ser
LRG_1197t1:c.194C>G
LRG_1197t2:c.101C>G
LRG_1197:g.32790C>G
LRG_1197p1:p.Thr65Ser
LRG_1197p2:p.Thr34Ser
NC_000009.11:g.36249252G>C

Protein change:

T34S

Molecular consequence:

NM_001190384.3:c.-13-2773C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001190388.2:c.-13-2773C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001374798.1:c.-13-2773C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001128227.3:c.194C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001190383.3:c.101C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374797.1:c.101C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005476.7:c.101C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: GNE myopathy (NM)
Synonyms:: Nonaka myopathy; Nonaka distal myopathy; INCLUSION BODY MYOPATHY, HEREDITARY, AUTOSOMAL RECESSIVE; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011603; MedGen: C1853926; Orphanet: 602; OMIM: 605820

Name:: Sialuria
Synonyms:: Sialic Acid Storage Disease; Sialuria, French type
Identifiers:: MONDO: MONDO:0010028; MedGen: C0342853; Orphanet: 3166; OMIM: 269921

Recent activity

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Homo sapiens WAPL cohesin release factor (WAPL), transcript variant 1, mRNA
Homo sapiens WAPL cohesin release factor (WAPL), transcript variant 1, mRNA
gi|971059207|ref|NM_015045.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003311525	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 18, 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

SCV003311525

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 18, 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, SCV003311525.2

#	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. 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. This variant has not been reported in the literature in individuals affected with GNE-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 65 of the GNE protein (p.Thr65Ser).

#	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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