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
hsa-mir-150 ENST00000602157 90.18 96.49 96.00 0.16 0.22 0.07 0.25 0.19 0.11
hsa-mir-1199 ENST00000269720 91.68 71.25 85.06 0.14 0.53 0.33 0.20 1.07 0.38
ZZZ3 ENST00000370801 17.14 4.53 8.19 1.44 3.25 2.58 0.86 0.32 0.37
ZZEF1 ENST00000381638 29.81 11.22 18.45 1.05 2.10 1.62 1.59 0.54 0.81
ZYX ENST00000322764 69.73 57.73 65.19 0.53 0.57 0.53 0.95 1.46 1.29
ZYG11B ENST00000294353 3.30 9.46 3.74 3.86 2.48 3.79 0.30 0.49 0.24
ZYG11A ENST00000371528 92.68 55.88 77.66 0.15 0.51 0.39 0.17 1.56 0.55
ZXDC ENST00000389709 46.94 53.35 49.05 0.57 0.66 0.72 1.82 1.70 1.83
ZXDB ENST00000374888 49.23 13.92 29.75 0.57 2.04 0.86 1.80 0.60 1.42
ZXDA ENST00000358697 72.53 62.15 69.54 0.32 0.53 0.44 0.80 1.35 0.96
ZWINT ENST00000373944 71.51 73.35 75.34 0.35 0.54 0.37 0.83 1.02 0.65
ZWILCH ENST00000307897 54.66 55.42 54.61 0.63 0.58 0.56 1.72 1.60 1.74
ZW10 ENST00000200135 32.35 26.82 27.75 0.99 1.23 0.90 1.71 1.12 1.27
ZUFSP ENST00000368576 35.42 53.37 42.72 0.97 0.66 0.68 1.87 1.70 2.02
ZSWIM8 ENST00000398706 2.17 2.29 0.74 4.17 3.65 4.59 0.27 0.29 0.20
ZSWIM7 ENST00000399277 45.30 66.60 55.63 0.62 0.54 0.53 1.77 1.22 1.73
ZSWIM6 ENST00000252744 18.93 0.37 7.00 1.58 4.13 2.88 0.94 0.28 0.33
ZSWIM5 ENST00000359600 19.79 18.25 16.86 1.54 1.49 1.70 0.99 0.74 0.70
ZSWIM4 ENST00000254323 51.37 29.26 38.59 0.59 1.14 0.84 1.85 1.35 2.01
ZSWIM3 ENST00000255152 26.68 43.05 33.02 1.30 0.61 0.85 1.33 1.89 1.66
ZSWIM2 ENST00000295131 59.75 69.43 66.26 0.58 0.56 0.52 1.40 1.13 1.20
ZSWIM1 ENST00000372523 41.46 85.85 65.09 0.82 0.28 0.51 1.68 0.43 1.31
ZSCAN9 ENST00000425468 78.54 70.64 77.78 0.34 0.51 0.38 0.66 1.08 0.55
ZSCAN5C ENST00000534327 95.34 84.30 92.56 0.10 0.28 0.14 0.11 0.44 0.15
ZSCAN5B ENST00000586855 97.62 92.68 97.73 0.10 0.29 0.09 0.11 0.30 0.05

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.