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
ALAS1 ENST00000394965 28.93 25.43 25.25 1.10 1.25 1.05 1.54 1.05 1.15
GPATCH2L ENST00000261530 28.93 29.66 27.43 1.10 1.10 0.96 1.54 1.39 1.27
ITFG1 ENST00000320640 28.94 22.17 23.66 1.10 1.52 1.16 1.54 0.81 1.01
SMC4 ENST00000357388 28.94 23.95 24.49 1.10 1.38 1.08 1.53 0.95 1.08
FLNB ENST00000490882 28.95 21.66 23.39 1.10 1.47 1.19 1.53 0.81 0.99
DUSP3 ENST00000226004 28.96 48.87 37.18 1.10 0.63 0.81 1.53 2.03 1.97
EMC1 ENST00000477853 28.96 55.13 40.30 1.10 0.57 0.80 1.53 1.63 2.00
TMEM62 ENST00000260403 28.97 57.60 41.53 1.10 0.57 0.75 1.53 1.48 2.02
CASZ1 ENST00000377022 28.97 3.00 13.65 1.10 3.46 2.01 1.53 0.28 0.57
TNFAIP3 ENST00000237289 28.98 5.28 14.89 1.10 3.11 1.94 1.53 0.32 0.63
GNPDA1 ENST00000508177 28.98 80.43 54.25 1.10 0.37 0.59 1.53 0.59 1.73
NCOA3 ENST00000371998 28.99 14.64 19.85 1.10 2.00 1.47 1.53 0.61 0.85
IDS ENST00000340855 28.99 4.70 14.57 1.10 3.26 1.99 1.53 0.31 0.59
KRT14 ENST00000167586 29.00 45.02 35.18 1.10 0.68 0.86 1.54 1.96 1.75
RET ENST00000355710 29.00 1.78 12.96 1.10 3.81 2.09 1.54 0.26 0.53
PIAS3 ENST00000393045 29.01 13.41 19.19 1.10 2.05 1.53 1.54 0.60 0.85
PRPF40A ENST00000410080 29.01 17.96 21.64 1.10 1.53 1.27 1.54 0.73 0.91
SEC61G ENST00000415949 29.02 50.28 37.91 1.10 0.67 0.85 1.55 1.97 2.01
CEP350 ENST00000367607 29.02 3.73 14.07 1.10 3.33 2.04 1.55 0.31 0.60
ABCA12 ENST00000272895 29.03 23.27 24.18 1.10 1.43 1.11 1.55 0.93 1.05
GPR52 ENST00000367685 29.03 48.79 37.17 1.10 0.63 0.81 1.54 2.02 1.97
OTUD4 ENST00000454497 29.04 6.53 15.61 1.10 2.63 1.76 1.54 0.37 0.66
PFDN4 ENST00000371419 29.04 44.68 35.03 1.10 0.66 0.87 1.54 1.98 1.75
FBXO5 ENST00000229758 29.05 8.27 16.48 1.10 2.54 1.71 1.54 0.45 0.69
TMEM108 ENST00000321871 29.05 5.62 15.11 1.10 2.97 1.86 1.54 0.33 0.63

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.