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
ANKS6 ENST00000353234 66.89 36.23 50.59 0.61 0.82 0.66 1.04 1.61 1.86
GABRQ ENST00000370306 66.90 38.34 51.77 0.61 0.75 0.62 1.04 1.72 1.93
OR2B2 ENST00000303324 66.90 70.18 70.91 0.61 0.53 0.43 1.04 1.12 0.86
SUN5 ENST00000356173 66.91 65.92 68.38 0.61 0.54 0.49 1.04 1.24 1.05
MAD1L1 ENST00000406869 66.91 52.02 59.92 0.61 0.61 0.49 1.04 1.86 1.63
HHIPL1 ENST00000330710 66.92 47.23 56.92 0.61 0.66 0.49 1.04 2.00 1.71
FAM72D ENST00000400889 66.92 87.45 80.51 0.61 0.23 0.39 1.04 0.40 0.51
SLC18B1 ENST00000275227 66.93 78.46 75.68 0.61 0.43 0.38 1.04 0.74 0.64
RSC1A1 ENST00000345034 66.93 79.33 76.19 0.61 0.38 0.37 1.04 0.67 0.62
KIAA0556 ENST00000261588 66.94 48.89 57.98 0.61 0.63 0.47 1.04 2.04 1.68
DPEP3 ENST00000268793 66.94 74.08 73.29 0.61 0.53 0.43 1.04 1.03 0.79
S100A2 ENST00000368708 66.95 96.83 85.24 0.61 0.23 0.34 1.04 0.19 0.36
RHCE ENST00000294413 66.95 37.80 51.53 0.61 0.80 0.62 1.03 1.70 1.92
UGT1A9 ENST00000354728 66.96 61.11 65.60 0.61 0.53 0.51 1.03 1.39 1.29
AKR7A2 ENST00000235835 66.96 79.29 76.18 0.61 0.38 0.37 1.03 0.67 0.62
MRPL46 ENST00000312475 66.97 74.16 73.34 0.61 0.53 0.43 1.03 1.03 0.78
C4orf46 ENST00000379205 66.97 89.03 81.36 0.61 0.27 0.38 1.03 0.35 0.49
NADSYN1 ENST00000319023 66.98 49.26 58.20 0.61 0.66 0.48 1.03 2.02 1.65
TMEM125 ENST00000432792 66.99 96.91 85.30 0.61 0.23 0.34 1.03 0.19 0.36
VEGFB ENST00000309422 66.99 92.88 83.30 0.61 0.29 0.32 1.03 0.30 0.40
OR52E4 ENST00000316987 67.00 95.95 84.84 0.61 0.22 0.34 1.03 0.20 0.40
MFRP ENST00000555262 67.00 66.21 68.59 0.61 0.53 0.47 1.03 1.21 1.05
PFKP ENST00000381125 67.01 62.18 66.27 0.61 0.52 0.52 1.03 1.35 1.20
HTRA4 ENST00000302495 67.01 67.59 69.47 0.61 0.53 0.44 1.03 1.19 0.98
RPUSD3 ENST00000383820 67.02 59.92 64.87 0.61 0.53 0.51 1.04 1.36 1.34

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.