Database of Pathogenic Variants

Individual Information

DPVS:10689.2

ID

DPVS:10689.2

Clinical Significance

Likely pathogenic

Date Last Evaluated

2019-03-29

Clinical Significance Citation

Mori-Yoshimura, M. Nationwide patient registry for GNE myopathy in Japan. 2014 Orphanet J Rare Dis. 2014 Oct 11;9:150. doi: 10.1186/s13023-014-0150-4. PMID:25303967

Mori-Yoshimura, M. 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. 2012 J Neurol Sci. 2012 Jul 15;318(1-2):100-5. doi: 10.1016/j.jns.2012.03.016. Epub 2012 Apr 14. PMID:22507750

Tajima, Y. Distal myopathy with rimmed vacuoles: impaired O-glycan formation in muscular glycoproteins. 2005 Am J Pathol. 2005 Apr;166(4):1121-30. doi: 10.1016/S0002-9440(10)62332-2. PMID:15793292

Noguchi, S. Reduction of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase activity and sialylation in distal myopathy with rimmed vacuoles. 2004 J Biol Chem. 2004 Mar 19;279(12):11402-7. doi: 10.1074/jbc.M313171200. Epub 2004 Jan 5. PMID:14707127

Nishino, I. Distal myopathy with rimmed vacuoles is allelic to hereditary inclusion body myopathy. 2002 Neurology. 2002 Dec 10;59(11):1689-93. doi: 10.1212/01.wnl.0000041631.28557.c6. PMID:12473753

Tomimitsu, H. Distal myopathy with rimmed vacuoles: novel mutations in the GNE gene. 2002 Neurology. 2002 Aug 13;59(3):451-4. doi: 10.1212/wnl.59.3.451. PMID:12177386

Transcript

Disease

Phenotype

Zygosity

compound heterozygote

Allele Origin

unknown

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

clinical testing

Compound heterozygous variant(s)

Data Submitter

Comment

c.[131G>C];[1985C>T]|c.[977G>A];[1985C>T]

VCF

VCF (GRCh37/hg19)

											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
9	36218221	NC_000009.11:g.36218221G>A	G	A	.	.	EXAC_AF=8.236e-05;EXAC_AC=10;EXAC_AN=121412;GNOMAD_AF=8.7481e-05;GNOMAD_AC=22;GNOMAD_AN=251482;CLNALLELEID=21074;CLNDN=Sialuria|GNE_myopathy|not_provided;CLNDISDB=MONDO:MONDO:0010028,MedGen:C0342853,OMIM:269921,Orphanet:ORPHA3166,SNOMED_CT:238051008|MONDO:MONDO:0011603,MedGen:C1853926,OMIM:605820,Orphanet:ORPHA602|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000009.11:g.36218221G>A;HGVD_AAF=0.000415;HGVD_NR=2411;HGVD_AC=1;GENEINFO=23657:10020;DPVID=9860;DPVSIG=Likely_pathogenic;DPVDSDBID=OMIM:605820;DPVDBN=Nonaka_myopathy;DPVHGVS=NC_000009.11:g.36218221G>A	.

VCF (GRCh38/hg38)

											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-qfphttd1>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
9	36218224	NC_000009.11:g.36218221G>A	G	A	.	.	dbSNP_RSID=rs62541771;GNOMAD_AF=8.7481e-05;GNOMAD_AC=22;GNOMAD_AN=251482;CLNALLELEID=21074;CLNDN=Sialuria|GNE_myopathy|not_provided;CLNDISDB=MONDO:MONDO:0010028,MedGen:C0342853,OMIM:269921,Orphanet:ORPHA3166,SNOMED_CT:238051008|MONDO:MONDO:0011603,MedGen:C1853926,OMIM:605820,Orphanet:ORPHA602|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000009.12:g.36218224G>A;GENEINFO=23657:10020;DPVID=9860;DPVSIG=Likely_pathogenic;DPVDSDBID=OMIM:605820;DPVDBN=Nonaka_myopathy;DPVHGVS=NC_000009.12:g.36218224G>A	.

Variant Detail