TABLE OF CONTENTS
Unfortunately, the Scientific Advisory Board for the Browser has insisted that the Locus Variants track be removed from the resident tracks. There is concern that the data on this track would be misinterpreted and lead to unwarranted actions by patients.
We disagree with this opinion, and we are in the process of ascertaining exactly what the concerns are and how they can be addressed more constructively. We hope that this perception of dangerous information will be discussed more widely and a better solution adopted.
As a work-around, we have established a PhenCode query page which allows you to easily load the Locus Variants data into the Genome Browser as a custom track. It also provides most of the filter settings from the original track, and we plan to augment this with additional query capabilities. Once you have loaded the custom track, the usual navigation and other features of the UCSC site are available as before, including operations with the Table Browser and display via Genome Graphs.
We remain committed to wide dissemination and easy availability of human variation data as recorded in LSDBs.
Status as of October 2012:
|Database||# Variants||# Track Items||Associated with|
|AD&FTDMD||370||373||Alzheimer disease, frontotemporal dementia|
|ARdb||493||493||AIS, Prostatic cancer|
|CA2base||24||24||Osteopetrosis with renal tubular acidosis|
|CASRdb||216||216||Familial (benign) hypocalciuric hypercalcemia (FHH)|
|CLCN7base||26||26||Autosomal dominant osteopetrosis, type 2|
|dbPEX||280||280||Peroxisome assembly diseases|
|dbRIP||2,771||2,771||Variety of human genetic diseases|
|F12base||2||2||Angioedema type III|
|Fanconi||754||754||Fanconi Anemia, birth defects, cancer|
|FHC Mutation Database (no longer online)||238||240||Familial hypertrophic cardiomyopathy|
|LOVD: The Globin Gene Server||251||251||Hemoglobinopathies|
|HIFD||1,137||1,155||Intermediate filament(76 distinct diseases)|
|ISTH SSC VWF||400||400||von Willebrand Factor|
|KinMutBase||566||566||Protein kinase domains|
|LQTSdb (no longer online)||265||269||Heart disease|
|OSTM1base||3||3||Autosomal recessive osteopetrosis|
|SRD5A2||42||42||Prostate and breast cancer|
|RPGR||345||345||X-linked retinitis pigmentosa (XLRP)|
Most LSDBs were updated in January, adding over 6,000 more variant positions since October 2010. In October 2012, the Swiss Prot Variants were updated adding almost 11,000 more variants.
This variant involves more than one change. The '..' shows that the parts of the HGVS-style name that do not describe this position have been left off. This is done to keep the labels short on the browser and to make it clear which mutation you are viewing.
The HGVS-style coding names all use the A of the ATG as position 1. Some of the LSDBs also use this as their starting point when assigning the common name, but some use other starting points.
First check the strand that is displayed and make sure it is the same strand as the variant's reference sequence (usually the same as a nearby gene). Also, for polymorphisms, the allele that is considered to be "wild type" is somewhat arbitrary. The nucleotide changes listed for a variant are based on the stated reference sequence used by the source LSDB, which may differ from the whole-genome assembly you are currently viewing in the Browser. The LSDB's reference sequence is often specified as part of the HGVS-style name.
Yes. The data and database table descriptions are available here.
Each database has its own unique traits, so the exact steps and the challenges met along the way will vary. We provide an example describing a fairly simple case.
The generic utility routines are freely available for use "as-is". A main script similar to this sample is also necessary, but must be customized for each data source.
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