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Protocols

HGVbase specifications

Information


Unique identifier OMICS_25504
Name HGVbase
Alternative names Human Genome Variation database, HGBASE (Human Genic Bi-Allelic SEquences)
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

Publications for Human Genome Variation database

HGVbase citations

 (9)
library_books

Predicting the functional consequences of non synonymous single nucleotide polymorphisms in IL8 gene

2017
Sci Rep
PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] ponding protein. These non-synonymous single nucleotide polymorphisms (nsSNPs) have been the subject of many recent studies and a large amount of data now exists in public repositories such as dbSNP, HGVBase and HGMD. The Swiss-Prot variant page and the ModSNP database provide a large resource for sequence and structure information on human protein variants. Identification of single nucleotide pol […]

call_split

A burden of rare variants in BMPR2 and KCNK3 contributes to a risk of familial pulmonary arterial hypertension

2017
PMCID: 5383973
PMID: 28388887
DOI: 10.1186/s12890-017-0400-z
call_split See protocol

[…] ignment, the variant call, and the variant quality score recalibration were analyzed using GATK []. The variants were called with an exome sequencing data set of 300 control samples obtained from the Human Genome Variation Database (accession ID: HGV0000004) []. The resulting VCF file has been deposited on the same database under accession HGV0000005. […]

library_books

A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene

2014
PMCID: 4156994
PMID: 25215231
DOI: 10.1155/2014/639751

[…] ccuracy accomplished by MutPred and PolyPhen2 depends on their specific criterion. Twelve structural and six sequence-based properties were used in this study (). About 28% of validated nsSNPs in the Human Genome Variation Database are predicted to affect protein function []. Similarly, about 25% of nsSNPs affecting protein activity was predicted by PolyPhen2 []. MutPred offers classification accu […]

library_books

Novel Hypoxanthine Guanine Phosphoribosyltransferase Gene Mutations in Saudi Arabian Hyperuricemia Patients

2014
Biomed Res Int
PMCID: 4119946
PMID: 25136576
DOI: 10.1155/2014/290325

[…] t are less accessible by conventional experimental methods. For MD simulations, the HPRT gene structural information was obtained from the PDB database (RCSB PDB) and Human Genome Variation database (HGVBASE). Based on the amino acid sequence and the ORF, the HPRT amino acid structure was submitted to I-TASSER program and the best among the five models based on the C-score (−3.452), TM-score (0.34 […]

library_books

Screening and structural evaluation of deleterious Non Synonymous SNPs of ePHA2 gene involved in susceptibility to cataract formation

2012
Bioinformation
PMCID: 3398778
PMID: 22829731
DOI: 10.6026/97320630008562

[…] l neutral, but others bringing deleterious effects to protein function and are responsible for many human genetic diseases [, ]. There are several databases with these variations of SNPs, such as the human genome variation database, HGVBase [], National Center for Biotechnology Information (NCBI) database, dbSNP [], and SWISSPROT []. The large size of these databases presents a challenging hurdle […]

library_books

In Silico Analysis of Single Nucleotide Polymorphism (SNPs) in Human β Globin Gene

2011
PLoS One
PMCID: 3197589
PMID: 22028795
DOI: 10.1371/journal.pone.0025876

[…] sm (dbSNP) (http://www.ncbi.nlm.nih.gov/SNP) , and from the single amino acid polymorphism database (SAAPdb) (http://www.bioinf.org.uk/saap/db/) , which is collected data on SNPs from both dbSNP and (Human Genome Variation database) HGVBASE that displays the data onto the translated regions of the gene to establish whether the mutation is in a region of the gene translated to protein (in exon) and […]

Citations

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HGVbase institution(s)
Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden; European Molecular Biology Laboratory, Heidelberg, Germany; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
HGVbase funding source(s)
Supported by the KI, EBI, EMBL, Pharmacia, Celera and Doubletwist.

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