Variant Detail

Variant Information
ID
DPV: 6748
Chromosome
X
Gene
HGVS (GRCh37/hg19)
NC_000023.10:g.107863584G>A
HGVS (GRCh38/hg38)
NC_000023.11:g.108620354G>A
HGVS (RNA)
NM_000495.3:c.2605G>A
HGVS (Protein)
NP_000486.1:p.G869R
dbSNP
-
ClinGen Allele Registry
CA258720
Allele Frequency
Individual Information

ID
DPVS:6782.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-22
Clinical Significance Citation
Yamamura, T. Natural History and Genotype-Phenotype Correlation in Female X-Linked Alport Syndrome. 2017 Kidney Int Rep. 2017 May 4;2(5):850-855. doi: 10.1016/j.ekir.2017.04.011. eCollection 2017 Sep. PMID:29270492

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:6809.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-22
Clinical Significance Citation
Yamamura, T. Natural History and Genotype-Phenotype Correlation in Female X-Linked Alport Syndrome. 2017 Kidney Int Rep. 2017 May 4;2(5):850-855. doi: 10.1016/j.ekir.2017.04.011. eCollection 2017 Sep. PMID:29270492

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:6889.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-22
Clinical Significance Citation
Yamamura, T. Natural History and Genotype-Phenotype Correlation in Female X-Linked Alport Syndrome. 2017 Kidney Int Rep. 2017 May 4;2(5):850-855. doi: 10.1016/j.ekir.2017.04.011. eCollection 2017 Sep. PMID:29270492

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:7732.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-28
Clinical Significance Citation
Yamamura, T. Natural History and Genotype-Phenotype Correlation in Female X-Linked Alport Syndrome. 2017 Kidney Int Rep. 2017 May 4;2(5):850-855. doi: 10.1016/j.ekir.2017.04.011. eCollection 2017 Sep. PMID:29270492

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:7758.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-28
Clinical Significance Citation
Yamamura, T. Natural History and Genotype-Phenotype Correlation in Female X-Linked Alport Syndrome. 2017 Kidney Int Rep. 2017 May 4;2(5):850-855. doi: 10.1016/j.ekir.2017.04.011. eCollection 2017 Sep. PMID:29270492

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:7837.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-28
Clinical Significance Citation
Yamamura, T. Natural History and Genotype-Phenotype Correlation in Female X-Linked Alport Syndrome. 2017 Kidney Int Rep. 2017 May 4;2(5):850-855. doi: 10.1016/j.ekir.2017.04.011. eCollection 2017 Sep. PMID:29270492

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:8687.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-29
Clinical Significance Citation
Hashimura, Y. Milder clinical aspects of X-linked Alport syndrome in men positive for the collagen IV alpha5 chain. 2014 Kidney Int. 2014 May;85(5):1208-13. doi: 10.1038/ki.2013.479. Epub 2013 Dec 4. PMID:24304881

Transcript
-
Disease

Phenotype
-
Zygosity
hemizygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
alpha5(IV)-negative group

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
X	107863584	NC_000023.10:g.107863584G>A	G	A	.	.	CLNALLELEID=35884;CLNDN=Alport_syndrome_1,_X-linked_recessive|Atypical_hemolytic_uremic_syndrome|Alport_syndrome|not_provided;CLNDISDB=MONDO:MONDO:0010520,MedGen:C4746986,OMIM:301050,Orphanet:ORPHA88917|MONDO:MONDO:0016244,MedGen:C2931788,OMIM:PS235400,Orphanet:ORPHA2134|MONDO:MONDO:0018965,MedGen:C1567741,OMIM:PS301050,Orphanet:ORPHA63|MedGen:CN517202;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000023.10:g.107863584G>A;GENEINFO=2207:1287;DPVID=6748;DPVSIG=Pathogenic;DPVDSDBID=OMIM:301050;DPVDBN=Alport_syndrome_1\x2c_X-linked;DPVHGVS=NC_000023.10:g.107863584G>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-n3fdj2x9>
##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
X	108620354	NC_000023.10:g.107863584G>A	G	A	.	.	dbSNP_RSID=rs104886189;CLNALLELEID=35884;CLNDN=Alport_syndrome_1,_X-linked_recessive|not_provided;CLNDISDB=MONDO:MONDO:0010520,MedGen:C4746986,OMIM:301050,Orphanet:ORPHA88917|MedGen:CN517202;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000023.11:g.108620354G>A;GENEINFO=2207:1287;DPVID=6748;DPVSIG=Pathogenic;DPVDSDBID=OMIM:301050;DPVDBN=Alport_syndrome_1\x2c_X-linked;DPVHGVS=NC_000023.11:g.108620354G>A	.