NM_005476.7(GNE):c.1760T>C (p.Ile587Thr) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Jan 9, 2024
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:: RCV000591867.31

Allele description [Variation Report for NM_005476.7(GNE):c.1760T>C (p.Ile587Thr)]

NM_005476.7(GNE):c.1760T>C (p.Ile587Thr)

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.1760T>C (p.Ile587Thr)

HGVS:

NC_000009.12:g.36219894A>G
NG_008246.1:g.62151T>C
NM_001128227.3:c.1853T>C
NM_001190383.3:c.1538T>C
NM_001190384.3:c.1430T>C
NM_001190388.2:c.1583T>C
NM_001374797.1:c.1607T>C
NM_001374798.1:c.1583T>C
NM_005476.7:c.1760T>CMANE SELECT
NP_001121699.1:p.Ile618Thr
NP_001177312.1:p.Ile513Thr
NP_001177313.1:p.Ile477Thr
NP_001177317.2:p.Ile528Thr
NP_001361726.1:p.Ile536Thr
NP_001361727.1:p.Ile528Thr
NP_005467.1:p.Ile587Thr
LRG_1197t1:c.1853T>C
LRG_1197t2:c.1760T>C
LRG_1197:g.62151T>C
LRG_1197p1:p.Ile618Thr
LRG_1197p2:p.Ile587Thr
NC_000009.11:g.36219891A>G
NM_001128227.2:c.1853T>C
NM_005476.5:c.1760T>C
NM_005476.7:c.1760T>C
Q9Y223:p.Ile587Thr

Protein change:

I477T

Links:

UniProtKB: Q9Y223#VAR_017961; dbSNP: rs748949603

NCBI 1000 Genomes Browser:

rs748949603

Molecular consequence:

NM_001128227.3:c.1853T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001190383.3:c.1538T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001190384.3:c.1430T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001190388.2:c.1583T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374797.1:c.1607T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374798.1:c.1583T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005476.7:c.1760T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000701266	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Jun 1, 2016)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12497639, 16503651, 20300792, 26627873 Citation Link,
SCV001248055	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Feb 1, 2023)	germline	clinical testing	Citation Link,
SCV002024881	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 2, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005325858	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 9, 2024)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations spectrum of GNE in hereditary inclusion body myopathy sparing the quadriceps.

Eisenberg I, Grabov-Nardini G, Hochner H, Korner M, Sadeh M, Bertorini T, Bushby K, Castellan C, Felice K, Mendell J, Merlini L, Shilling C, Wirguin I, Argov Z, Mitrani-Rosenbaum S.

Hum Mutat. 2003 Jan;21(1):99.

PubMed [citation]

PMID:: 12497639

Influence of UDP-GlcNAc 2-epimerase/ManNAc kinase mutant proteins on hereditary inclusion body myopathy.

Penner J, Mantey LR, Elgavish S, Ghaderi D, Cirak S, Berger M, Krause S, Lucka L, Voit T, Mitrani-Rosenbaum S, Hinderlich S.

Biochemistry. 2006 Mar 7;45(9):2968-77.

PubMed [citation]

PMID:: 16503651

See all PubMed Citations (5)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000701266.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	germline	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001248055.25

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

Description

GNE: PM3:Strong, PM1, PM2, PP4:Moderate, PP2

#	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		2	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002024881.3

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV005325858.1

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

Description

Published functional studies demonstrate that the variant results in impaired protein function (PMID: 16503651); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24796702, 31561939, 19917666, 22231866, 27854221, 29431110, 32403337, 33250842, 33197058, 35138478, 35723113, 26231298, 24695763, 26627873, 16503651, 29480215, 35503500, 12497639, 35398442)

#	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

Last Updated: Oct 8, 2024

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