Variant Detail

Variant Information
ID
DPV: 12038
Chromosome
12
Gene
HGVS (GRCh37/hg19)
NC_000012.11:g.48387611G>A
HGVS (GRCh38/hg38)
NC_000012.12:g.47993828G>A
HGVS (RNA)
NM_001844.5:c.905C>T
HGVS (Protein)
NP_001835.3:p.A302V
dbSNP
-
ClinGen Allele Registry
CA384521889
Allele Frequency
Individual Information

ID
DPVS:13296.2
Clinical Significance
Pathogenic
Date Last Evaluated
2020-07-03
Clinical Significance Citation
Bogaert, R. Expression, in cartilage, of a 7-amino-acid deletion in type II collagen from two unrelated individuals with Kniest dysplasia. 1994 Am J Hum Genet. 1994 Dec;55(6):1128-36. PMID:7977371

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
de novo
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
This variant was detected in  IRUD (Initiative on Rare and Undiagnosed Diseases) project.

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
12	48387611	NC_000012.11:g.48387611G>A	G	A	.	.	CLNALLELEID=445013;CLNDN=Spondyloepiphyseal_dysplasia_congenita|Spondyloepimetaphyseal_dysplasia,_Strudwick_type|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002655,Human_Phenotype_Ontology:HP:0002776,Human_Phenotype_Ontology:HP:0005893,MONDO:MONDO:0008471,MedGen:C2745959,OMIM:183900,Orphanet:ORPHA94068|MONDO:MONDO:0008476,MedGen:C0700635,OMIM:184250,Orphanet:ORPHA93346,SNOMED_CT:702350003|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000012.11:g.48387611G>A;GENEINFO=2200:1280;DPVID=12038;DPVSIG=Pathogenic;DPVDSDBID=OMIM:108300;DPVDBN=Stickler_syndrome_1;DPVHGVS=NC_000012.11:g.48387611G>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-crrs4wu6>
##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
12	47993828	NC_000012.11:g.48387611G>A	G	A	.	.	CLNALLELEID=445013;CLNDN=Spondyloepiphyseal_dysplasia_congenita|Spondylometaphyseal_dysplasia|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0002655,Human_Phenotype_Ontology:HP:0002776,Human_Phenotype_Ontology:HP:0005893,MONDO:MONDO:0008471,MedGen:C0038015,OMIM:183900,Orphanet:ORPHA94068|Human_Phenotype_Ontology:HP:0002657,MedGen:C4759767,OMIM:184250|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000012.12:g.47993828G>A;GENEINFO=2200:1280;DPVID=12038;DPVSIG=Pathogenic;DPVDSDBID=OMIM:108300;DPVDBN=Stickler_syndrome_1;DPVHGVS=NC_000012.12:g.47993828G>A	.