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
ORC3 ENST00000257789 38.74 37.16 36.08 0.92 0.78 0.87 1.75 1.66 1.79
MMP2 ENST00000219070 38.75 16.47 25.69 0.92 1.78 1.04 1.75 0.69 1.22
SLC39A1 ENST00000368623 38.75 42.31 38.85 0.92 0.61 0.81 1.75 1.89 2.05
C1orf172 ENST00000320567 38.76 36.84 35.90 0.92 0.76 0.86 1.75 1.66 1.78
PDIA6 ENST00000272227 38.76 20.03 27.52 0.92 1.43 0.96 1.76 0.73 1.27
B4GALNT1 ENST00000341156 38.77 40.78 38.04 0.92 0.62 0.85 1.76 1.78 2.02
ACAT1 ENST00000265838 38.77 57.10 46.63 0.92 0.56 0.66 1.76 1.49 1.87
ATP6V0A2 ENST00000330342 38.78 39.61 37.45 0.92 0.68 0.86 1.76 1.65 2.01
RILPL1 ENST00000376874 38.78 24.05 29.57 0.91 1.37 0.84 1.77 0.96 1.39
ERP29 ENST00000261735 38.79 26.14 30.75 0.91 1.20 0.78 1.76 1.08 1.49
CMTM3 ENST00000424011 38.79 88.69 65.21 0.91 0.25 0.53 1.76 0.35 1.29
TMEM138 ENST00000278826 38.80 60.70 48.63 0.91 0.54 0.67 1.75 1.40 1.85
SEMA5B ENST00000451055 38.80 31.07 33.09 0.91 1.04 0.87 1.75 1.36 1.66
APOA1BP ENST00000368235 38.81 72.54 55.29 0.91 0.47 0.51 1.75 1.04 1.73
ST6GALNAC3 ENST00000328299 38.82 47.68 41.49 0.91 0.61 0.73 1.75 1.97 2.02
SASS6 ENST00000287482 38.82 36.49 35.76 0.91 0.80 0.85 1.75 1.64 1.78
EPB41L2 ENST00000337057 38.83 11.30 23.17 0.91 2.13 1.19 1.75 0.55 1.01
ADAMTS3 ENST00000286657 38.83 29.62 32.41 0.91 1.10 0.91 1.75 1.39 1.61
NPR3 ENST00000265074 38.84 43.31 39.41 0.91 0.61 0.78 1.75 1.93 2.04
NCAPD2 ENST00000315579 38.84 31.04 33.09 0.91 1.04 0.87 1.74 1.35 1.67
TP53 ENST00000269305 38.85 31.81 33.49 0.91 0.94 0.89 1.73 1.48 1.72
TNNI2 ENST00000381906 38.85 42.53 39.04 0.91 0.59 0.78 1.73 1.87 2.06
CBY1 ENST00000396811 38.86 78.63 58.84 0.91 0.40 0.51 1.73 0.74 1.65
NOSTRIN ENST00000444448 38.86 58.67 47.53 0.91 0.54 0.63 1.74 1.43 1.89
FBXO46 ENST00000317683 38.87 21.70 28.45 0.91 1.46 0.78 1.74 0.81 1.29

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.