PhenCode: Frequently asked questions


Why can't I find the Locus Variants track on the UCSC Genome Browser?

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.

What data sources are included in the Locus Variants track, and how many entries does it contain?

Status as of October 2012:

Database# Variants# Track ItemsAssociated with
AD&FTDMD 370373 Alzheimer disease, frontotemporal dementia
ALPL 252252 Hypophosphatasia
ARdb 493493 AIS, Prostatic cancer
BGMUT 7622,174 Blood groups
CA2base 2424 Osteopetrosis with renal tubular acidosis
CASRdb 216216 Familial (benign) hypocalciuric hypercalcemia (FHH)
CBS 151151 CBS Deficiency
CFMDB 1,8921,893 Cystic fibrosis
CLCN7base 2626 Autosomal dominant osteopetrosis, type 2
dbPEX 280280 Peroxisome assembly diseases
dbRIP 2,7712,771 Variety of human genetic diseases
F12base 22 Angioedema type III
Fanconi 754754 Fanconi Anemia, birth defects, cancer
FHC Mutation Database (no longer online) 238240 Familial hypertrophic cardiomyopathy
LOVD: The Globin Gene Server 251251 Hemoglobinopathies
HbVar 1,4841,740 Hemoglobinopathies
HIFD 1,1371,155 Intermediate filament(76 distinct diseases)
IARC TP53 4,1734,173 Cancer
IDbases 3,0303,030 Immune deficiencies
IPNMDB 8981000 Peripheral neuropathies
ISTH SSC VWF 400400 von Willebrand Factor
KinMutBase 566566 Protein kinase domains
LMDp 7,5837,583 Muscular dystrophy
LQTSdb (no longer online) 265269 Heart disease
MMR 2,1032,262 Lynch syndrome
OSTM1base 33 Autosomal recessive osteopetrosis
PAHdb 547552 Phenylketonuria
RettBASE 868868 Rett syndrome
RISN 1,7081,708 Retinal disorders
SRD5A24242 Prostate and breast cancer
RPGR 345345 X-linked retinitis pigmentosa (XLRP)
X-ALD 579579 X-linked Adrenoleukodystrophy
LSDB TOTALS34,21336,175
Swiss-Prot 56,39656,918

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.

What do the '..' in the HGVS-style names mean?

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.

Why do the HGVS name and the common name indicate different positions for the variant?

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.

Why doesn't the reference nucleotide listed in the substitution match the nucleotide in the Browser?

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.

Can I download the data from PhenCode?

Yes. The data and database table descriptions are available here.

What are the steps for adding a newly contributed data source to the track?

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.

How can I obtain the programs used to convert from coordinates in a database's reference sequence to chromosome coordinates?

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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