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
ZC3H12D ENST00000409806 78.51 39.55 59.24 0.34 0.68 0.49 0.66 1.65 1.68
TEX11 ENST00000395889 78.52 0.62 37.78 0.34 4.14 0.84 0.66 0.28 2.01
OR4C12 ENST00000335238 78.52 90.97 87.85 0.34 0.25 0.24 0.66 0.35 0.32
ZNF474 ENST00000296600 78.53 68.12 76.44 0.34 0.52 0.38 0.66 1.20 0.61
TYSND1 ENST00000287078 78.53 55.13 68.84 0.34 0.57 0.46 0.66 1.63 1.05
FAM173A ENST00000569529 78.54 78.69 81.99 0.34 0.40 0.37 0.66 0.73 0.47
ZSCAN9 ENST00000425468 78.54 70.64 77.78 0.34 0.51 0.38 0.66 1.08 0.55
TPO ENST00000345913 78.55 59.76 71.71 0.34 0.52 0.46 0.66 1.37 0.82
SLC9A3R1 ENST00000262613 78.55 63.14 73.63 0.34 0.47 0.40 0.66 1.31 0.74
ENTPD1 ENST00000371207 78.56 32.17 54.95 0.34 0.86 0.51 0.66 1.46 1.74
PTH2 ENST00000270631 78.57 96.29 90.48 0.34 0.22 0.14 0.66 0.19 0.21
PGAM4 ENST00000458128 78.57 99.88 91.97 0.34 0.17 0.14 0.66 0.11 0.16
DUSP23 ENST00000368107 78.58 89.93 87.39 0.34 0.25 0.28 0.66 0.37 0.31
FAM65C ENST00000327979 78.58 55.10 68.90 0.34 0.57 0.46 0.66 1.63 1.04
CD84 ENST00000311224 78.59 67.53 76.08 0.34 0.54 0.38 0.66 1.20 0.62
RETN ENST00000221515 78.59 88.58 86.76 0.34 0.24 0.30 0.66 0.35 0.31
RP11-315D16.2 ENST00000562767 78.60 85.00 85.15 0.34 0.25 0.33 0.66 0.45 0.37
OGFOD3 ENST00000329197 78.60 68.69 76.75 0.34 0.53 0.34 0.66 1.18 0.61
SOX4 ENST00000244745 78.61 16.20 46.13 0.34 1.80 0.67 0.66 0.70 1.97
OR4X1 ENST00000320048 78.61 93.82 89.32 0.34 0.27 0.18 0.66 0.26 0.25
SLC35E2B ENST00000378662 78.62 59.89 71.82 0.34 0.53 0.44 0.66 1.36 0.82
RGL3 ENST00000393423 78.62 72.86 79.03 0.34 0.49 0.39 0.66 1.05 0.54
CD83 ENST00000379153 78.63 52.65 67.42 0.34 0.68 0.52 0.66 1.81 1.14
SCIMP ENST00000574081 78.63 77.39 81.37 0.35 0.42 0.38 0.66 0.76 0.49
TAS2R39 ENST00000446620 78.64 95.08 89.93 0.35 0.23 0.18 0.65 0.21 0.23

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.