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
UNCX ENST00000316333 14.08 35.29 22.84 1.63 0.76 1.19 0.71 1.58 0.97
BRWD3 ENST00000373275 14.09 0.04 4.33 1.63 4.10 3.75 0.71 0.26 0.24
DENND5A ENST00000328194 14.09 17.72 13.53 1.63 1.53 2.05 0.71 0.73 0.57
HS3ST2 ENST00000261374 14.10 45.96 28.21 1.63 0.76 0.81 0.71 2.02 1.28
MACF1 ENST00000545844 14.10 0.66 4.74 1.63 4.11 3.68 0.71 0.28 0.25
RPS6KA5 ENST00000261991 14.11 4.06 6.40 1.63 3.24 3.06 0.71 0.32 0.32
JMJD1C ENST00000399262 14.11 0.40 4.58 1.63 4.15 3.70 0.71 0.28 0.25
ITPKA ENST00000260386 14.12 17.63 13.50 1.62 1.58 2.05 0.71 0.73 0.57
GLA ENST00000218516 14.12 4.36 6.62 1.62 3.27 3.00 0.71 0.32 0.32
GARNL3 ENST00000373387 14.13 24.88 17.38 1.62 1.33 1.64 0.71 1.05 0.75
MED14 ENST00000324817 14.13 0.93 4.79 1.62 4.10 3.67 0.71 0.29 0.24
EMC2 ENST00000220853 14.14 28.51 19.32 1.62 1.15 1.53 0.71 1.25 0.85
TRIM13 ENST00000356017 14.14 18.35 13.94 1.62 1.49 2.06 0.71 0.75 0.59
CNIH1 ENST00000216416 14.15 32.20 21.30 1.62 0.86 1.39 0.71 1.46 0.91
TESPA1 ENST00000449076 14.15 39.69 24.97 1.62 0.66 1.02 0.71 1.66 1.14
HTRA2 ENST00000258080 14.16 40.01 25.15 1.62 0.63 1.05 0.71 1.68 1.16
UBA1 ENST00000335972 14.16 1.61 5.15 1.62 3.87 3.59 0.71 0.26 0.25
RHOBTB3 ENST00000379982 14.17 38.23 24.21 1.62 0.76 1.11 0.71 1.70 1.05
TCP1 ENST00000321394 14.17 9.05 8.97 1.62 2.43 2.47 0.71 0.47 0.38
ATP5G1 ENST00000393366 14.18 51.01 30.86 1.62 0.65 0.77 0.71 1.92 1.49
RUNX1 ENST00000300305 14.18 17.81 13.67 1.62 1.52 2.02 0.71 0.72 0.57
SLC32A1 ENST00000217420 14.19 13.68 11.60 1.62 2.06 2.23 0.71 0.59 0.45
RNF165 ENST00000269439 14.19 9.13 9.03 1.62 2.47 2.42 0.71 0.47 0.38
CLK3 ENST00000395066 14.20 22.04 15.96 1.62 1.48 1.77 0.72 0.81 0.66
OLIG2 ENST00000333337 14.20 71.14 40.86 1.62 0.51 0.80 0.72 1.06 2.06

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.