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
YJEFN3 ENST00000514277 84.07 68.78 79.70 0.30 0.53 0.38 0.48 1.19 0.53
HCAR3 ENST00000528880 84.07 95.63 92.58 0.30 0.23 0.14 0.48 0.21 0.15
ZNF577 ENST00000301399 84.08 58.47 74.11 0.30 0.54 0.39 0.48 1.39 0.69
IFNW1 ENST00000380229 84.08 98.11 93.95 0.30 0.20 0.09 0.48 0.16 0.11
MZT2B ENST00000281871 84.09 83.54 87.02 0.30 0.27 0.28 0.48 0.47 0.30
ATP5I ENST00000304312 84.09 72.88 81.86 0.30 0.49 0.37 0.48 1.04 0.46
CCDC116 ENST00000292779 84.10 68.35 79.49 0.30 0.52 0.38 0.48 1.21 0.52
ATP8B3 ENST00000310127 84.10 53.95 71.55 0.30 0.65 0.44 0.48 1.70 0.83
R3HDM4 ENST00000361574 84.11 59.48 74.74 0.30 0.51 0.40 0.48 1.40 0.67
PRSS58 ENST00000552471 84.11 90.63 90.42 0.32 0.25 0.15 0.48 0.36 0.21
RAD51AP2 ENST00000399080 84.12 65.74 78.18 0.32 0.54 0.39 0.47 1.22 0.55
PPAN-P2RY11 ENST00000393796 84.12 63.28 76.82 0.32 0.47 0.35 0.47 1.31 0.61
PPAN ENST00000556468 84.13 63.34 76.83 0.32 0.48 0.35 0.47 1.31 0.61
LCN6 ENST00000341206 84.13 79.71 85.27 0.32 0.37 0.34 0.47 0.64 0.36
DUSP21 ENST00000339042 84.14 96.86 93.21 0.32 0.23 0.14 0.48 0.19 0.15
ARHGAP23 ENST00000431231 84.14 5.95 43.41 0.32 2.82 0.63 0.48 0.35 2.00
SPOCD1 ENST00000360482 84.15 42.40 64.60 0.32 0.59 0.51 0.48 1.90 1.32
CST3 ENST00000398411 84.15 83.05 86.77 0.32 0.30 0.30 0.48 0.49 0.31
BID ENST00000317361 84.16 95.30 92.42 0.32 0.23 0.14 0.48 0.21 0.15
SPP2 ENST00000168148 84.16 92.91 91.44 0.32 0.29 0.15 0.48 0.30 0.18
NFE2L3 ENST00000056233 84.17 71.76 81.32 0.32 0.51 0.38 0.47 1.07 0.48
OR4K13 ENST00000315693 84.17 95.37 92.46 0.32 0.24 0.14 0.47 0.21 0.15
FAM149B1 ENST00000242505 84.18 57.87 73.81 0.32 0.57 0.42 0.47 1.48 0.71
OXER1 ENST00000378661 84.18 97.38 93.55 0.32 0.22 0.13 0.47 0.19 0.15
SH3TC1 ENST00000245105 84.19 69.51 80.21 0.32 0.54 0.37 0.47 1.11 0.52

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.