NM_005476.7(GNE):c.1892C>T (p.Ala631Val) AND not provided

Germline classification:: Pathogenic (6 submissions)
Last evaluated:: Jun 21, 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:: RCV000254883.36

Allele description [Variation Report for NM_005476.7(GNE):c.1892C>T (p.Ala631Val)]

NM_005476.7(GNE):c.1892C>T (p.Ala631Val)

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.1892C>T (p.Ala631Val)

HGVS:

NC_000009.12:g.36218224G>A
NG_008246.1:g.63821C>T
NM_001128227.3:c.1985C>T
NM_001190383.3:c.1670C>T
NM_001190384.3:c.1562C>T
NM_001190388.2:c.1715C>T
NM_001374797.1:c.1739C>T
NM_001374798.1:c.1715C>T
NM_005476.7:c.1892C>TMANE SELECT
NP_001121699.1:p.Ala662Val
NP_001177312.1:p.Ala557Val
NP_001177313.1:p.Ala521Val
NP_001177317.2:p.Ala572Val
NP_001361726.1:p.Ala580Val
NP_001361727.1:p.Ala572Val
NP_005467.1:p.Ala631Val
LRG_1197t1:c.1985C>T
LRG_1197t2:c.1892C>T
LRG_1197:g.63821C>T
LRG_1197p1:p.Ala662Val
LRG_1197p2:p.Ala631Val
NC_000009.11:g.36218221G>A
NM_001128227.2:c.1985C>T
NM_005476.7:c.1892C>T

Protein change:

A521V; ALA631VAL

Links:

OMIM: 603824.0015; dbSNP: rs62541771

NCBI 1000 Genomes Browser:

rs62541771

Molecular consequence:

NM_001128227.3:c.1985C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001190383.3:c.1670C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001190384.3:c.1562C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001190388.2:c.1715C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374797.1:c.1739C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374798.1:c.1715C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005476.7:c.1892C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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NADH dehydrogenase subunit 7 (chloroplast) [Corymbia eximia]
NADH dehydrogenase subunit 7 (chloroplast) [Corymbia eximia]
gi|545718967|ref|YP_008577804.1|

Protein
PREDICTED: Homo sapiens zinc finger protein 302 (ZNF302), transcript variant X7,...
PREDICTED: Homo sapiens zinc finger protein 302 (ZNF302), transcript variant X7, mRNA
gi|2217321999|ref|XM_017026982.2|

Nucleotide
Mystus cavasius isolate CIFRI.MC-14 cytochrome b (cytb) gene, partial cds; mitoc...
Mystus cavasius isolate CIFRI.MC-14 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|2288000461|gb|ON715379.1|

Nucleotide
Mystus cavasius isolate CIFRI.NAIH.MC-29 cytochrome b (cytb) gene, partial cds; ...
Mystus cavasius isolate CIFRI.NAIH.MC-29 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|2567179050|gb|OR113075.1|

Nucleotide
Mystus cavasius isolate CIFRI.NAIH.MC-26 cytochrome b (cytb) gene, partial cds; ...
Mystus cavasius isolate CIFRI.NAIH.MC-26 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|2567179048|gb|OR113074.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000321742	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 21, 2024)	germline	clinical testing	Citation Link,
SCV000331895	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Apr 3, 2018)	germline	clinical testing	Citation Link,
SCV000613535	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Jan 24, 2017)	germline	clinical testing	PubMed (25) [See all records that cite these PMIDs] 12177386, 24695763, 22507750, 14707127, 16503651, 15987957, 12473769, 12497639, 22196754, 25123033, 17261181, 26968811, 21131200, 19841673, 15793292, 25303967, 21517694, 14972325, 21307865, 22883483, 20059379, 16112887, 22343627, 12473753, 26467025
SCV001248054	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2019)	germline	clinical testing	Citation Link,
SCV002024869	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 24, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004226607	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 18, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 14707127, 15987957, 24695763, 35138478, 25741868

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	14	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Distal myopathy with rimmed vacuoles: novel mutations in the GNE gene.

Tomimitsu H, Ishikawa K, Shimizu J, Ohkoshi N, Kanazawa I, Mizusawa H.

Neurology. 2002 Aug 13;59(3):451-4.

PubMed [citation]

PMID:: 12177386

Heterozygous UDP-GlcNAc 2-epimerase and N-acetylmannosamine kinase domain mutations in the GNE gene result in a less severe GNE myopathy phenotype compared to homozygous N-acetylmannosamine kinase domain mutations.

Mori-Yoshimura M, Monma K, Suzuki N, Aoki M, Kumamoto T, Tanaka K, Tomimitsu H, Nakano S, Sonoo M, Shimizu J, Sugie K, Nakamura H, Oya Y, Hayashi YK, Malicdan MC, Noguchi S, Murata M, Nishino I.

J Neurol Sci. 2012 Jul 15;318(1-2):100-5. doi: 10.1016/j.jns.2012.03.016. Epub 2012 Apr 14.

PubMed [citation]

PMID:: 22507750

See all PubMed Citations (27)

Details of each submission

From GeneDx, SCV000321742.10

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

Description

Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34676965, 19917666, 15987957, 22507750, 12177386, 16503651, 31127727, 35138478, 26968811, 24796702, 38674419, 37510394, 24695763, 14707127)

#	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 Eurofins Ntd Llc (ga), SCV000331895.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	13	not provided	not provided	clinical testing	not provided

#	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		13	not provided	not provided	not provided

From Athena Diagnostics, SCV000613535.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (25)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV001248054.26

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

#	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, SCV002024869.3

#	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 Mayo Clinic Laboratories, Mayo Clinic, SCV004226607.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (5)

Description

PP3, PM2, PM3_strong, PS3, PS4

#	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		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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