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
ADAT3 ENST00000329478 88.59 70.69 82.98 0.20 0.49 0.32 0.34 1.09 0.40
C5AR1 ENST00000355085 88.59 87.72 91.10 0.20 0.24 0.15 0.34 0.37 0.20
CA6 ENST00000377436 88.60 47.02 70.03 0.20 0.68 0.47 0.34 1.98 0.91
OR6C68 ENST00000548615 88.60 96.21 95.12 0.20 0.22 0.09 0.34 0.20 0.10
RP11-664I21.6 ENST00000524433 88.61 85.61 90.16 0.20 0.27 0.18 0.34 0.44 0.21
MUC19 ENST00000454784 88.61 53.26 73.73 0.20 0.66 0.42 0.34 1.73 0.71
SPRR2G ENST00000368748 88.62 99.05 96.17 0.20 0.15 0.07 0.34 0.14 0.10
PRAC1 ENST00000290294 88.62 95.46 94.74 0.20 0.24 0.09 0.34 0.20 0.11
ZNF98 ENST00000357774 88.63 83.54 89.18 0.20 0.27 0.19 0.34 0.47 0.25
ARMCX4 ENST00000423738 88.63 2.02 43.68 0.20 3.73 0.61 0.34 0.29 2.02
ZNF324B ENST00000336614 88.64 59.96 77.51 0.19 0.53 0.35 0.34 1.37 0.57
SPATA12 ENST00000334325 88.64 98.71 96.59 0.19 0.18 0.08 0.34 0.15 0.07
C1QTNF8 ENST00000328449 88.65 97.31 95.76 0.19 0.23 0.07 0.34 0.19 0.11
POTEI ENST00000451531 88.65 91.31 92.73 0.19 0.23 0.14 0.34 0.34 0.15
DDX60L ENST00000260184 88.66 54.35 74.39 0.19 0.61 0.40 0.34 1.68 0.71
CTAGE15 ENST00000420911 88.66 97.86 96.05 0.19 0.21 0.07 0.34 0.17 0.11
FRMD1 ENST00000283309 88.67 71.84 83.64 0.19 0.51 0.33 0.34 1.07 0.40
EME2 ENST00000568449 88.67 96.54 95.34 0.19 0.22 0.08 0.34 0.19 0.10
NKX3-2 ENST00000382438 88.68 33.87 62.03 0.19 0.84 0.48 0.34 1.55 1.44
DARC ENST00000368121 88.68 84.62 89.75 0.19 0.27 0.18 0.34 0.42 0.23
WFDC13 ENST00000305479 88.69 80.76 87.84 0.19 0.37 0.24 0.34 0.57 0.32
RP11-766F14.2 ENST00000511828 88.69 35.50 63.18 0.19 0.77 0.49 0.34 1.57 1.37
FAM111A ENST00000528737 88.70 96.81 95.52 0.19 0.23 0.08 0.34 0.19 0.11
SERPINA12 ENST00000341228 88.70 81.19 88.10 0.19 0.35 0.23 0.33 0.54 0.30
C19orf71 ENST00000329493 88.71 92.45 93.28 0.19 0.27 0.13 0.33 0.30 0.15

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.