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
PPRC1 ENST00000278070 28.28 3.10 13.31 1.18 3.45 2.05 1.48 0.28 0.55
RUSC2 ENST00000455600 28.29 9.74 16.85 1.18 2.43 1.70 1.48 0.50 0.70
PARD6B ENST00000371610 28.29 16.37 20.42 1.18 1.80 1.51 1.49 0.69 0.88
AARS ENST00000261772 28.30 33.56 29.07 1.18 0.85 0.84 1.49 1.53 1.32
CEP76 ENST00000262127 28.30 39.65 32.19 1.18 0.68 0.91 1.49 1.65 1.60
ITGA2B ENST00000262407 28.31 40.16 32.44 1.18 0.62 0.91 1.49 1.72 1.61
LHX5 ENST00000261731 28.31 15.70 20.07 1.18 1.87 1.49 1.49 0.68 0.86
ADAD1 ENST00000296513 28.32 24.28 24.38 1.18 1.30 1.08 1.49 0.99 1.07
NFRKB ENST00000524794 28.32 16.79 20.68 1.18 1.67 1.47 1.50 0.71 0.88
DAPK1 ENST00000408954 28.33 10.78 17.44 1.18 2.11 1.62 1.50 0.51 0.76
C4orf32 ENST00000309733 28.34 44.97 34.84 1.18 0.68 0.90 1.50 1.97 1.75
IDI1 ENST00000381344 28.34 59.49 42.16 1.18 0.51 0.68 1.50 1.40 2.01
EVI5 ENST00000370331 28.35 39.84 32.30 1.18 0.65 0.90 1.50 1.68 1.61
CLDN7 ENST00000360325 28.35 67.16 46.40 1.19 0.54 0.67 1.50 1.23 1.90
SLC24A3 ENST00000328041 28.36 16.26 20.38 1.18 1.78 1.49 1.50 0.69 0.88
CDIPT ENST00000219789 28.36 38.94 31.86 1.18 0.70 0.92 1.50 1.64 1.58
POU1F1 ENST00000344265 28.37 37.56 31.18 1.18 0.80 0.85 1.50 1.68 1.55
WBSCR17 ENST00000333538 28.37 24.67 24.60 1.18 1.29 1.06 1.51 1.04 1.10
RNF103 ENST00000237455 28.38 17.05 20.87 1.18 1.62 1.47 1.51 0.74 0.87
FIZ1 ENST00000221665 28.38 30.38 27.49 1.18 1.08 0.97 1.51 1.39 1.27
DIS3L2 ENST00000325385 28.39 14.56 19.47 1.18 2.04 1.53 1.51 0.61 0.84
ZMPSTE24 ENST00000372759 28.39 71.40 48.78 1.18 0.53 0.70 1.51 1.05 1.86
LRRC16B ENST00000342740 28.40 24.16 24.32 1.18 1.33 1.09 1.51 0.99 1.07
MRPS36 ENST00000256441 28.40 68.77 47.32 1.18 0.53 0.66 1.50 1.18 1.87
SFN ENST00000339276 28.41 40.23 32.51 1.18 0.61 0.89 1.50 1.72 1.62

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.