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
ZNF546 ENST00000347077 75.10 51.87 64.90 0.38 0.59 0.51 0.77 1.87 1.33
ZNF547 ENST00000282282 94.92 91.59 95.99 0.10 0.23 0.07 0.12 0.33 0.11
ZNF548 ENST00000336128 86.65 58.48 75.51 0.24 0.54 0.38 0.41 1.39 0.66
ZNF549 ENST00000376233 88.83 85.25 90.10 0.19 0.25 0.18 0.33 0.46 0.22
ZNF550 ENST00000506609 83.91 91.30 90.66 0.29 0.23 0.15 0.48 0.34 0.20
ZNF551 ENST00000282296 97.02 82.71 92.62 0.10 0.34 0.14 0.11 0.50 0.15
ZNF552 ENST00000391701 95.04 94.12 97.27 0.10 0.25 0.08 0.12 0.25 0.07
ZNF554 ENST00000317243 88.01 66.76 80.71 0.22 0.56 0.39 0.35 1.22 0.52
ZNF555 ENST00000334241 81.31 56.84 71.63 0.33 0.56 0.44 0.60 1.54 0.83
ZNF556 ENST00000307635 96.76 84.93 93.61 0.11 0.27 0.13 0.11 0.44 0.15
ZNF557 ENST00000414706 85.91 50.07 70.24 0.27 0.67 0.43 0.45 1.99 0.91
ZNF558 ENST00000601372 46.05 61.22 53.04 0.58 0.53 0.61 1.80 1.40 1.87
ZNF559 ENST00000393883 95.21 90.91 95.80 0.10 0.25 0.07 0.12 0.35 0.11
ZNF560 ENST00000301480 98.50 61.60 83.41 0.10 0.54 0.33 0.11 1.41 0.40
ZNF561 ENST00000302851 95.91 85.45 93.40 0.11 0.25 0.11 0.11 0.45 0.15
ZNF562 ENST00000448622 99.32 60.85 83.43 0.11 0.56 0.33 0.12 1.41 0.40
ZNF563 ENST00000293725 87.08 32.93 60.49 0.23 0.82 0.44 0.38 1.46 1.58
ZNF564 ENST00000339282 85.07 58.13 74.52 0.28 0.53 0.40 0.46 1.46 0.69
ZNF565 ENST00000392173 48.58 43.91 44.89 0.51 0.61 0.68 1.80 1.97 2.04
ZNF566 ENST00000454319 33.96 25.49 27.88 0.92 1.25 0.85 1.76 1.06 1.29
ZNF567 ENST00000585696 38.32 54.11 44.84 0.91 0.65 0.67 1.73 1.68 2.04
ZNF568 ENST00000333987 53.65 51.27 51.60 0.62 0.65 0.62 1.76 1.90 1.94
ZNF569 ENST00000316950 47.58 52.72 49.06 0.56 0.66 0.72 1.80 1.80 1.83
ZNF57 ENST00000306908 97.68 81.36 92.21 0.10 0.33 0.14 0.10 0.54 0.16
ZNF570 ENST00000330173 31.00 39.44 33.38 0.96 0.70 0.87 1.68 1.64 1.72

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.