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
C16orf89 ENST00000315997 85.10 85.13 88.30 0.28 0.25 0.22 0.46 0.45 0.30
PKIB ENST00000258014 85.10 86.44 88.90 0.28 0.24 0.19 0.46 0.42 0.28
CD1B ENST00000368168 85.11 72.83 82.37 0.28 0.49 0.33 0.46 1.04 0.44
KLLN ENST00000445946 85.11 94.31 92.40 0.28 0.24 0.14 0.46 0.25 0.15
NEU4 ENST00000325935 85.12 82.48 86.99 0.28 0.34 0.28 0.46 0.52 0.30
ZNF177 ENST00000434737 85.12 61.86 76.58 0.28 0.57 0.37 0.46 1.35 0.61
GIMAP1 ENST00000307194 85.13 85.81 88.59 0.28 0.28 0.22 0.46 0.44 0.28
HBZ ENST00000252951 85.14 94.16 92.33 0.28 0.25 0.14 0.46 0.25 0.15
HTR3E ENST00000440596 85.14 84.07 87.76 0.28 0.27 0.24 0.46 0.45 0.32
FAM71B ENST00000302938 85.15 71.65 81.78 0.28 0.53 0.37 0.46 1.07 0.47
TSPAN10 ENST00000328585 85.15 90.19 90.74 0.28 0.25 0.15 0.46 0.38 0.20
GALNTL5 ENST00000392800 85.16 84.49 87.98 0.28 0.29 0.24 0.46 0.44 0.32
ZSCAN10 ENST00000252463 85.16 41.21 64.49 0.28 0.61 0.51 0.46 1.83 1.33
OR2T7 ENST00000460972 85.17 91.02 91.05 0.28 0.25 0.15 0.46 0.36 0.20
TAS2R5 ENST00000247883 85.17 82.31 86.94 0.28 0.34 0.29 0.46 0.53 0.31
CD320 ENST00000301458 85.18 69.01 80.40 0.28 0.54 0.38 0.46 1.15 0.50
OR4A16 ENST00000314721 85.18 92.39 91.62 0.28 0.25 0.14 0.46 0.30 0.18
DPP7 ENST00000371579 85.19 79.18 85.52 0.28 0.39 0.33 0.46 0.69 0.35
FAM103A1 ENST00000304191 85.19 73.54 82.76 0.28 0.53 0.32 0.47 1.03 0.42
CCDC74B ENST00000310463 85.20 77.18 84.53 0.28 0.43 0.33 0.47 0.78 0.39
CCDC15 ENST00000344762 85.20 57.48 74.20 0.28 0.56 0.39 0.47 1.48 0.69
EGFL7 ENST00000371699 85.21 94.71 92.72 0.28 0.23 0.14 0.47 0.24 0.15
TMEM261 ENST00000358227 85.21 93.99 92.28 0.28 0.25 0.14 0.47 0.26 0.15
C2orf54 ENST00000388934 85.22 79.77 85.80 0.28 0.37 0.33 0.47 0.64 0.33
ZP4 ENST00000366570 85.22 71.62 81.81 0.28 0.53 0.37 0.47 1.07 0.46

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.