NM_005476.7(GNE):c.388del (p.Ile130fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 5, 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:: RCV002530723.3

Allele description [Variation Report for NM_005476.7(GNE):c.388del (p.Ile130fs)]

NM_005476.7(GNE):c.388del (p.Ile130fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_005476.7(GNE):c.388del (p.Ile130fs)

HGVS:

NC_000009.12:g.36246260del
NG_008246.1:g.35786del
NM_001128227.2:c.481del
NM_001128227.3:c.481del
NM_001190383.3:c.388del
NM_001190384.3:c.211del
NM_001190388.2:c.211del
NM_001374797.1:c.388del
NM_001374798.1:c.211del
NM_005476.7:c.388delMANE SELECT
NP_001121699.1:p.Ile161fs
NP_001177312.1:p.Ile130fs
NP_001177313.1:p.Ile71fs
NP_001177317.2:p.Ile71fs
NP_001361726.1:p.Ile130fs
NP_001361727.1:p.Ile71fs
NP_005467.1:p.Ile130fs
LRG_1197t1:c.481del
LRG_1197t2:c.388del
LRG_1197:g.35786del
LRG_1197p1:p.Ile161fs
LRG_1197p2:p.Ile130fs
NC_000009.11:g.36246256del
NC_000009.11:g.36246257del
NM_001128227.2:c.481delA

Protein change:

I130fs

Links:

dbSNP: rs1423445315

NCBI 1000 Genomes Browser:

rs1423445315

Molecular consequence:

NM_001128227.3:c.481del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001190383.3:c.388del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001190384.3:c.211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001190388.2:c.211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374797.1:c.388del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374798.1:c.211del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005476.7:c.388del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003476636	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24027297, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003476636

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 5, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Mutation profile of the GNE gene in Japanese patients with distal myopathy with rimmed vacuoles (GNE myopathy).

Cho A, Hayashi YK, Monma K, Oya Y, Noguchi S, Nonaka I, Nishino I.

J Neurol Neurosurg Psychiatry. 2014 Aug;85(8):914-7. doi: 10.1136/jnnp-2013-305587. Epub 2013 Sep 11.

PubMed [citation]

PMID:: 24027297

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, SCV003476636.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 552473). This variant has not been reported in the literature in individuals affected with GNE-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Ile161Serfs*21) in the GNE gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNE are known to be pathogenic (PMID: 24027297).

#	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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