GeVIR Banner

Export Results to CSV Clear Search

Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
BECN1 ENST00000361523 23.76 16.18 17.90 1.34 1.81 1.68 1.12 0.69 0.78
LHFP ENST00000379589 23.77 29.93 24.90 1.35 1.11 1.02 1.12 1.41 1.11
UBQLN2 ENST00000338222 23.77 21.51 20.79 1.37 1.42 1.47 1.12 0.80 0.88
FOXB1 ENST00000396057 23.78 18.17 18.97 1.37 1.49 1.54 1.12 0.74 0.83
SLC39A13 ENST00000362021 23.78 41.05 30.64 1.37 0.59 0.80 1.12 1.81 1.47
TFG ENST00000240851 23.79 25.60 22.86 1.37 1.25 1.19 1.12 1.05 0.97
DKK2 ENST00000285311 23.80 23.45 21.75 1.37 1.42 1.25 1.12 0.93 0.93
ALG9 ENST00000531154 23.80 33.05 26.52 1.37 0.85 0.99 1.12 1.49 1.25
ACKR3 ENST00000272928 23.81 36.82 28.51 1.37 0.76 0.78 1.12 1.66 1.31
SLC30A7 ENST00000370112 23.81 55.91 38.17 1.35 0.51 0.85 1.12 1.56 2.05
PCDH20 ENST00000409186 23.82 14.62 17.08 1.35 2.01 1.67 1.12 0.61 0.72
SLC22A4 ENST00000200652 23.82 55.72 38.05 1.35 0.52 0.85 1.12 1.60 2.02
PHYHIPL ENST00000373880 23.83 20.70 20.33 1.37 1.47 1.48 1.12 0.80 0.88
HDGF ENST00000368206 23.83 32.85 26.44 1.37 0.84 1.00 1.12 1.44 1.25
SYNJ1 ENST00000433931 23.84 13.20 16.33 1.37 2.06 1.71 1.12 0.60 0.67
DHRS3 ENST00000376223 23.84 35.16 27.66 1.37 0.76 0.95 1.12 1.58 1.27
B3GAT3 ENST00000265471 23.85 73.34 47.34 1.37 0.54 0.66 1.12 1.02 1.87
SLC20A2 ENST00000342228 23.85 13.98 16.79 1.37 2.06 1.70 1.12 0.60 0.70
TAT ENST00000355962 23.86 33.40 26.78 1.37 0.84 0.96 1.12 1.51 1.27
SPNS1 ENST00000311008 23.86 30.17 25.09 1.37 1.10 1.05 1.12 1.41 1.17
DLG5 ENST00000372391 23.87 9.27 14.28 1.37 2.47 2.01 1.12 0.46 0.60
SLC25A22 ENST00000320230 23.87 36.56 28.41 1.37 0.78 0.78 1.12 1.63 1.30
MCMBP ENST00000360003 23.88 10.48 14.98 1.37 2.23 1.87 1.11 0.50 0.63
SLITRK5 ENST00000325089 23.88 16.85 18.30 1.37 1.66 1.67 1.11 0.71 0.79
CSTF2T ENST00000331173 23.89 31.22 25.62 1.37 1.00 1.06 1.11 1.37 1.21

Cookies disclaimer

I agree Our site saves small pieces of text information (cookies) on your device in order to deliver better content and for statistical purposes. You can disable the usage of cookies by changing the settings of your browser. By browsing our website without changing the browser settings you grant us permission to store that information on your device.