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Protocols

HUMSAVAR specifications

Information


Unique identifier OMICS_04128
Name HUMSAVAR
Restrictions to use None
Maintained No

Taxon


  • Primates
    • Homo sapiens

HUMSAVAR citations

 (15)
library_books

Prediction and interpretation of deleterious coding variants in terms of protein structural stability

2018
Sci Rep
PMCID: 5852127
PMID: 29540703
DOI: 10.1038/s41598-018-22531-2

[…] The training dataset was built by combining the annotated, non-synonymous SNV data from three different databases: DbSNP, SwissVar and HumSaVar. In a first stage, we combined all SNVs while avoiding repeats. Note that variants occurring in more than one database with different neutral/deleterious annotation were discarded. The SNVs w […]

call_split

Development of pathogenicity predictors specific for variants that do not comply with clinical guidelines for the use of computational evidence

2017
BMC Genomics
PMCID: 5558188
PMID: 28812538
DOI: 10.1186/s12864-017-3914-0
call_split See protocol

[…] ogical and neutral variants, was obtained following commonly used procedures [, , ]. Pathological variants were retrieved from UniProt [] and corresponded to sequence variants labeled as “Disease” in Humsavar (version 06-JUL-2016). However, not all of them were included in our initial dataset; we removed those variants from proteins contributing less than 30 independent variants to Humsavar. For e […]

library_books

eDGAR: a database of Disease Gene Associations with annotated Relationships among genes

2017
BMC Genomics
PMCID: 5558190
PMID: 28812536
DOI: 10.1186/s12864-017-3911-3

[…] ractory congestive heart failure, or stridor.In eDGAR the familial isolated hypoparathyroidism (OMIM 146200) is associated with three different genes: GCM2 and PTH (both reported in OMIM, ClinVar and Humsavar) and CASR (reported only in ClinVar). CASR is an extracellular calcium-sensing receptor whose activity is mediated by G-proteins, PTH is the parathyroid hormone, whose function is to increase […]

library_books

High confidence assessment of functional impact of human mitochondrial non synonymous genome variations by APOGEE

2017
PLoS Comput Biol
PMCID: 5501658
PMID: 28640805
DOI: 10.1371/journal.pcbi.1005628

[…] ed and larger training set. Most classifiers were indeed trained on a handful of known variations, as for example, MToolBox DS, which was built on the 53 damaging missense variants available from the Humsavar dataset (Table 3 in []). On the contrary, APOGEE was trained on a total of 223 deleterious variants. […]

call_split

A knowledge based framework for the discovery of cancer predisposing variants using large scale sequencing breast cancer data

2017
PMCID: 5452392
PMID: 28569218
DOI: 10.1186/s13058-017-0854-1
call_split See protocol

[…] Interpretation of Variants in Cancer (CiViC) [], Database of Curated Mutations (DoCM) [], Catalogue of Somatic Mutations in Cancer (COSMIC) [], cBioPortal []) and in databases of pathogenic variants (HumSavar [], ClinVar []). Cancer-related pathogenic variants are used in particular to define a set of prototype in Results – age-dependent polygenic model (Additional file : Table S5). Gene, protein […]

library_books

Variant effect prediction tools assessed using independent, functional assay based datasets: implications for discovery and diagnostics

2017
Hum Genomics
PMCID: 5433009
PMID: 28511696
DOI: 10.1186/s40246-017-0104-8

[…] raining and validation (or ‘benchmarking’) of these algorithms has been conducted using datasets that list variants with assigned classifications. Commonly used datasets include HumDiv [], HumVar [], Humsavar [], EPS [], dbSNP [] and HGMD []. All of the above algorithms have reported potential merit and are widely used in practice. The original publication of REVEL, for example, reported that when […]


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