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
ZSCAN5A ENST00000587340 99.34 53.70 79.84 0.11 0.63 0.37 0.12 1.69 0.52
ZSCAN4 ENST00000318203 88.51 83.22 88.97 0.20 0.28 0.19 0.34 0.47 0.28
ZSCAN32 ENST00000304926 87.04 81.16 87.28 0.23 0.35 0.28 0.39 0.55 0.31
ZSCAN31 ENST00000414429 77.03 62.09 72.22 0.34 0.56 0.43 0.72 1.36 0.82
ZSCAN30 ENST00000420878 67.35 70.61 71.50 0.58 0.51 0.46 1.04 1.08 0.85
ZSCAN29 ENST00000396976 43.85 47.68 44.25 0.75 0.61 0.62 1.78 1.97 2.05
ZSCAN25 ENST00000394152 48.06 38.46 41.50 0.54 0.75 0.73 1.79 1.70 2.02
ZSCAN23 ENST00000289788 31.51 74.67 52.36 0.95 0.54 0.61 1.69 0.96 1.90
ZSCAN22 ENST00000329665 80.60 67.87 77.44 0.32 0.52 0.35 0.58 1.18 0.57
ZSCAN21 ENST00000292450 30.98 77.46 53.64 0.96 0.42 0.63 1.67 0.76 1.80
ZSCAN20 ENST00000361328 32.90 25.59 27.37 0.94 1.25 0.96 1.70 1.05 1.27
ZSCAN2 ENST00000448803 51.74 44.18 46.65 0.58 0.62 0.66 1.82 1.95 1.87
ZSCAN18 ENST00000600404 45.11 35.66 38.65 0.63 0.78 0.82 1.75 1.57 2.01
ZSCAN16 ENST00000340487 55.89 76.86 68.33 0.57 0.43 0.49 1.63 0.81 1.07
ZSCAN12 ENST00000361028 22.75 45.97 32.56 1.44 0.76 0.89 1.05 2.02 1.62
ZSCAN10 ENST00000252463 85.16 41.21 64.49 0.28 0.61 0.51 0.46 1.83 1.33
ZSCAN1 ENST00000282326 88.14 83.51 88.94 0.20 0.27 0.19 0.35 0.46 0.28
ZRSR2 ENST00000307771 39.65 3.03 19.34 0.90 3.47 1.53 1.75 0.28 0.85
ZRSR1 ENST00000391338 87.97 74.74 84.75 0.22 0.54 0.34 0.35 0.96 0.40
ZRANB3 ENST00000264159 71.14 50.00 61.25 0.42 0.66 0.43 0.86 2.01 1.48
ZRANB2 ENST00000370920 1.29 4.67 1.16 4.39 3.27 4.42 0.17 0.31 0.20
ZRANB1 ENST00000359653 6.76 8.68 4.98 2.97 2.48 3.69 0.37 0.48 0.25
ZPLD1 ENST00000306176 49.76 55.28 51.67 0.54 0.57 0.62 1.84 1.62 1.94
ZPBP2 ENST00000348931 65.65 53.97 60.26 0.58 0.65 0.47 1.08 1.70 1.60
ZPBP ENST00000046087 27.57 41.69 32.81 1.23 0.61 0.85 1.41 1.80 1.65

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.