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
HIST1H4D ENST00000340756 68.96 96.78 86.11 0.57 0.23 0.33 0.95 0.19 0.33
AQP6 ENST00000315520 68.96 63.81 68.36 0.57 0.49 0.49 0.95 1.21 1.05
AKIP1 ENST00000309377 68.97 81.87 78.67 0.57 0.35 0.38 0.95 0.51 0.54
IL17RB ENST00000288167 68.97 62.97 67.87 0.57 0.49 0.51 0.95 1.31 1.12
POLN ENST00000511885 68.98 75.36 75.10 0.57 0.48 0.39 0.95 0.89 0.67
DTWD2 ENST00000510708 68.98 83.60 79.55 0.57 0.27 0.38 0.95 0.47 0.52
KIAA0753 ENST00000361413 68.99 61.44 66.95 0.57 0.54 0.53 0.95 1.40 1.19
METTL25 ENST00000248306 68.99 57.94 64.87 0.57 0.57 0.51 0.95 1.46 1.34
SCRT1 ENST00000332135 69.00 48.99 59.18 0.57 0.65 0.49 0.96 2.04 1.68
C11orf63 ENST00000227349 69.00 50.05 59.95 0.57 0.66 0.49 0.96 2.00 1.62
MGRN1 ENST00000262370 69.01 20.26 43.00 0.57 1.43 0.67 0.96 0.75 2.01
OBSCN ENST00000570156 69.02 45.45 57.11 0.57 0.70 0.52 0.96 1.99 1.70
GNG8 ENST00000300873 69.02 87.70 81.74 0.57 0.24 0.35 0.96 0.37 0.47
NOX1 ENST00000372966 69.03 57.97 64.93 0.57 0.56 0.51 0.96 1.45 1.33
ADORA3 ENST00000369716 69.03 63.27 68.13 0.57 0.47 0.49 0.96 1.31 1.09
C15orf43 ENST00000340827 69.04 73.60 74.16 0.57 0.52 0.39 0.96 1.03 0.69
EME1 ENST00000393271 69.04 68.86 71.46 0.57 0.54 0.46 0.96 1.18 0.86
POLR3K ENST00000293860 69.05 68.50 71.24 0.57 0.52 0.44 0.96 1.20 0.86
FAM187A ENST00000331733 69.05 77.05 76.07 0.57 0.42 0.38 0.96 0.78 0.62
CXCL12 ENST00000395794 69.06 63.77 68.41 0.57 0.49 0.47 0.96 1.22 1.06
ALS2CR12 ENST00000405148 69.06 77.56 76.41 0.57 0.42 0.38 0.96 0.79 0.62
CD180 ENST00000256447 69.07 54.99 63.08 0.57 0.57 0.49 0.95 1.64 1.39
STK19 ENST00000375333 69.07 65.58 69.50 0.57 0.53 0.44 0.95 1.22 0.97
PMFBP1 ENST00000237353 69.08 59.92 66.17 0.57 0.53 0.52 0.95 1.36 1.20
ERAP2 ENST00000437043 69.08 64.84 69.04 0.57 0.48 0.44 0.96 1.24 1.03

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.