NM_005476.7(GNE):c.1622T>C (p.Ile541Thr) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 27, 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:: RCV001374233.6

Allele description [Variation Report for NM_005476.7(GNE):c.1622T>C (p.Ile541Thr)]

NM_005476.7(GNE):c.1622T>C (p.Ile541Thr)

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.1622T>C (p.Ile541Thr)

HGVS:

NC_000009.12:g.36222788A>G
NG_008246.1:g.59257T>C
NM_001128227.3:c.1715T>C
NM_001190383.3:c.1411+585T>C
NM_001190384.3:c.1292T>C
NM_001190388.2:c.1445T>C
NM_001374797.1:c.1469T>C
NM_001374798.1:c.1445T>C
NM_005476.7:c.1622T>CMANE SELECT
NP_001121699.1:p.Ile572Thr
NP_001177313.1:p.Ile431Thr
NP_001177317.2:p.Ile482Thr
NP_001361726.1:p.Ile490Thr
NP_001361727.1:p.Ile482Thr
NP_005467.1:p.Ile541Thr
LRG_1197t1:c.1715T>C
LRG_1197t2:c.1622T>C
LRG_1197:g.59257T>C
LRG_1197p1:p.Ile572Thr
LRG_1197p2:p.Ile541Thr
NC_000009.11:g.36222785A>G
NM_001128227.2:c.1715T>C

Protein change:

I431T

Links:

dbSNP: rs369119154

NCBI 1000 Genomes Browser:

rs369119154

Molecular consequence:

NM_001190383.3:c.1411+585T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001128227.3:c.1715T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001190384.3:c.1292T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001190388.2:c.1445T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374797.1:c.1469T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374798.1:c.1445T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005476.7:c.1622T>C - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001571031	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 27, 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

SCV001571031

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 27, 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, SCV001571031.3

#	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 isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 572 of the GNE protein (p.Ile572Thr). This variant is present in population databases (rs369119154, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with GNE-related conditions. ClinVar contains an entry for this variant (Variation ID: 1064281). 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: Sep 29, 2024

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