Variant Detail

Variant Information
ID
DPV: 9869
Chromosome
9
Gene
HGVS (GRCh37/hg19)
NC_000009.11:g.36219937C>G
HGVS (GRCh38/hg38)
NC_000009.12:g.36219940C>G
HGVS (RNA)
NM_001128227.2:c.1807G>C
HGVS (Protein)
NP_001121699.1:p.V603L
dbSNP
-
ClinGen Allele Registry
CA274932
Allele Frequency
Individual Information

ID
DPVS:10773.2
Clinical Significance
Likely pathogenic
Date Last Evaluated
2019-03-29
Clinical Significance Citation
Ghilardi, G. [Latero-lateral choledochoduodenostomy in benign pathology of the common bile duct. A prospective study]. 1990 Minerva Chir. 1990 Jun 30;45(12):843-7. PMID:2250775
Tomimitsu, H. Distal myopathy with rimmed vacuoles (DMRV): new GNE mutations and splice variant. 2004 Neurology. 2004 May 11;62(9):1607-10. doi: 10.1212/01.wnl.0000123115.23652.6c. PMID:15136692
Arai, A. A novel mutation in the GNE gene and a linkage disequilibrium in Japanese pedigrees. 2002 Ann Neurol. 2002 Oct;52(4):516-9. doi: 10.1002/ana.10341. PMID:12325084
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
Kayashima, T. Nonaka myopathy is caused by mutations in the UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase gene (GNE). 2002 J Hum Genet. 2002;47(2):77-9. doi: 10.1007/s100380200004. PMID:11916006

Transcript
-
Disease

Phenotype
-
Zygosity
homozygote
Allele Origin
unknown
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:10778.1
Clinical Significance
Likely pathogenic
Date Last Evaluated
2019-03-29
Clinical Significance Citation
Kayashima, T. Nonaka myopathy is caused by mutations in the UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase gene (GNE). 2002 J Hum Genet. 2002;47(2):77-9. doi: 10.1007/s100380200004. PMID:11916006
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

Transcript
  • NM_001128227.2
Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
unknown
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
c.[115C>T];[1807G>C]|c.[131G>C];[1807G>C]|c.[179T>G];[1807G>C]|c.[188_197dup];[1807G>C]|c.[395G>A];[1807G>C]|c.[476dupT];[1807G>C]|c.[622C>T];[1807G>C]|c.[653A>G];[1807G>C]|c.[662T>C];[1807G>C]|c.[710-4A>G];[1807G>C]|c.[830G>A];[1807G>C]|c.[862+4A>G];[1807G>C]|c.[902T>C];[1807G>C]|c.[922C>G];[1807G>C]|c.[976G>C];[1807G>C]|c.[1163+5G>T];[1807G>C]|c.[1351C>T];[1807G>C]|c.[1355T>C];[1807G>C] and etc.

ClinVar
Model Animals
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	36219937	NC_000009.11:g.36219937C>G	C	G	.	.	EXAC_AF=2.471e-05;EXAC_AC=3;EXAC_AN=121412;GNOMAD_AF=1.5905e-05;GNOMAD_AC=4;GNOMAD_AN=251490;TOMMO_4_7K_AF=0.0007;TOMMO_4_7K_AC=7;TOMMO_4_7K_AN=9546;CLNALLELEID=21072;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.36219937C>G;HGVD_AAF=0.001653;HGVD_NR=2416;HGVD_AC=4;GENEINFO=23657:10020;DPVID=9869;DPVSIG=Likely_pathogenic;DPVDSDBID=OMIM:605820;DPVDBN=Nonaka_myopathy;DPVHGVS=NC_000009.11:g.36219937C>G	.
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-_ooy_9eh>
##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	36219940	NC_000009.11:g.36219937C>G	C	G	.	.	dbSNP_RSID=rs121908632;GNOMAD_AF=1.5905e-05;GNOMAD_AC=4;GNOMAD_AN=251490;CLNALLELEID=21072;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.36219940C>G;GENEINFO=23657:10020;DPVID=9869;DPVSIG=Likely_pathogenic;DPVDSDBID=OMIM:605820;DPVDBN=Nonaka_myopathy;DPVHGVS=NC_000009.12:g.36219940C>G	.