NM_005476.7(GNE):c.31C>T (p.Arg11Trp) AND GNE myopathy

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Apr 30, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000665671.10

Allele description [Variation Report for NM_005476.7(GNE):c.31C>T (p.Arg11Trp)]

NM_005476.7(GNE):c.31C>T (p.Arg11Trp)

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.31C>T (p.Arg11Trp)

HGVS:

NC_000009.12:g.36249325G>A
NG_008246.1:g.32720C>T
NM_001128227.3:c.124C>T
NM_001190383.3:c.31C>T
NM_001190384.3:c.-13-2843C>T
NM_001190388.2:c.-13-2843C>T
NM_001374797.1:c.31C>T
NM_001374798.1:c.-13-2843C>T
NM_005476.7:c.31C>TMANE SELECT
NP_001121699.1:p.Arg42Trp
NP_001177312.1:p.Arg11Trp
NP_001361726.1:p.Arg11Trp
NP_005467.1:p.Arg11Trp
LRG_1197t1:c.124C>T
LRG_1197t2:c.31C>T
LRG_1197:g.32720C>T
LRG_1197p1:p.Arg42Trp
LRG_1197p2:p.Arg11Trp
NC_000009.11:g.36249322G>A
NM_001128227.2:c.124C>T

Protein change:

R11W

Links:

dbSNP: rs769716748

NCBI 1000 Genomes Browser:

rs769716748

Molecular consequence:

NM_001190384.3:c.-13-2843C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001190388.2:c.-13-2843C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001374798.1:c.-13-2843C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001128227.3:c.124C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001190383.3:c.31C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374797.1:c.31C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005476.7:c.31C>T - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000789830	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Feb 22, 2017)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 14972325, 25617006, 17698786, 16503651 Citation Link,
SCV003807685	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 16, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004191648	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 30, 2023)	unknown	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

SCV000789830

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Feb 22, 2017)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV003807685

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 16, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004191648

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 30, 2023)

unknown

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Hypoglycosylation of alpha-dystroglycan in patients with hereditary IBM due to GNE mutations.

Huizing M, Rakocevic G, Sparks SE, Mamali I, Shatunov A, Goldfarb L, Krasnewich D, Gahl WA, Dalakas MC.

Mol Genet Metab. 2004 Mar;81(3):196-202.

PubMed [citation]

PMID:: 14972325

Targeted sequencing and identification of genetic variants in sporadic inclusion body myositis.

Weihl CC, Baloh RH, Lee Y, Chou TF, Pittman SK, Lopate G, Allred P, Jockel-Balsarotti J, Pestronk A, Harms MB.

Neuromuscul Disord. 2015 Apr;25(4):289-96. doi: 10.1016/j.nmd.2014.12.009. Epub 2015 Jan 6.

PubMed [citation]

PMID:: 25617006
PMCID:: PMC4372452

See all PubMed Citations (5)

Details of each submission

From Counsyl, SCV000789830.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003807685.2

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

Description

ACMG classification criteria: PS3 supporting, PS4 moderated, PM2 moderated, PM3 moderated, PM5 moderated, PP3 supporting

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004191648.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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