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
NSA2 ENST00000296802 50.24 39.39 43.18 0.57 0.70 0.65 1.80 1.65 1.99
CDK5RAP2 ENST00000349780 50.24 34.05 40.41 0.57 0.82 0.80 1.80 1.55 2.02
BCL9L ENST00000334801 50.25 9.29 27.92 0.57 2.48 0.85 1.80 0.47 1.29
MIPEP ENST00000382172 50.25 57.35 53.26 0.57 0.54 0.61 1.81 1.49 1.87
CCKBR ENST00000334619 50.26 57.86 53.47 0.57 0.57 0.63 1.81 1.47 1.82
SLC15A2 ENST00000489711 50.26 56.60 52.76 0.57 0.53 0.61 1.81 1.55 1.89
C2 ENST00000299367 50.27 58.41 53.77 0.57 0.54 0.62 1.81 1.39 1.80
TMEM182 ENST00000412401 50.27 41.09 44.09 0.57 0.59 0.61 1.81 1.81 2.03
SLCO2A1 ENST00000310926 50.28 60.19 54.81 0.57 0.52 0.53 1.81 1.38 1.74
STARD6 ENST00000581310 50.28 65.13 57.67 0.57 0.49 0.49 1.80 1.24 1.66
KLHL26 ENST00000300976 50.29 54.39 51.48 0.57 0.62 0.63 1.80 1.66 1.91
HAX1 ENST00000328703 50.29 74.80 63.80 0.57 0.53 0.49 1.80 0.95 1.38
FAM71F1 ENST00000315184 50.30 66.53 58.48 0.57 0.57 0.51 1.80 1.22 1.65
RP9 ENST00000297157 50.30 52.24 50.32 0.57 0.62 0.66 1.80 1.84 1.92
EIF2AK1 ENST00000199389 50.31 37.05 41.90 0.57 0.78 0.68 1.81 1.68 2.01
ALOXE3 ENST00000318227 50.31 56.98 53.07 0.57 0.56 0.61 1.82 1.53 1.87
TMEM69 ENST00000372025 50.32 83.33 68.84 0.57 0.27 0.46 1.82 0.47 1.05
AHCTF1 ENST00000326225 50.32 2.15 24.28 0.57 3.67 1.10 1.82 0.29 1.06
RABAC1 ENST00000222008 50.33 57.83 53.48 0.57 0.57 0.63 1.82 1.48 1.82
SFXN4 ENST00000355697 50.33 50.58 49.32 0.57 0.63 0.70 1.82 1.94 1.84
KIAA1407 ENST00000295878 50.34 68.65 59.90 0.57 0.53 0.49 1.82 1.18 1.63
C5orf34 ENST00000306862 50.34 61.22 55.44 0.57 0.53 0.51 1.82 1.40 1.72
PTGER2 ENST00000245457 50.35 45.46 46.58 0.57 0.70 0.66 1.82 1.99 1.89
TMCO2 ENST00000372766 50.35 80.68 67.31 0.58 0.37 0.52 1.82 0.56 1.15
DEFB104A ENST00000314265 50.36 93.36 74.76 0.58 0.28 0.40 1.82 0.28 0.66

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.