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
MAPT ENST00000344290 13.95 28.68 19.31 1.61 1.16 1.53 0.71 1.29 0.85
PPAT ENST00000264220 13.96 12.71 10.97 1.61 2.10 2.21 0.71 0.58 0.44
VAPA ENST00000340541 13.96 30.59 20.35 1.61 1.08 1.49 0.71 1.39 0.88
CCL19 ENST00000311925 13.97 74.78 42.67 1.61 0.54 0.68 0.71 0.96 2.02
IQCJ-SCHIP1 ENST00000485419 13.97 26.70 18.27 1.61 1.19 1.66 0.71 1.12 0.79
NDUFS7 ENST00000233627 13.98 16.82 12.98 1.61 1.66 2.09 0.71 0.71 0.53
RBM7 ENST00000540163 13.98 26.52 18.20 1.61 1.19 1.66 0.71 1.12 0.79
MDGA2 ENST00000439988 13.99 16.55 12.81 1.61 1.78 2.11 0.71 0.69 0.52
GNG12 ENST00000370982 13.99 58.11 34.35 1.61 0.53 0.87 0.71 1.46 1.77
AGAP2-AS1 ENST00000542466 14.00 57.83 34.08 1.61 0.57 0.91 0.71 1.48 1.74
ATP1B1 ENST00000367816 14.00 3.73 6.13 1.62 3.34 3.23 0.71 0.30 0.30
TAF5 ENST00000369839 14.01 7.20 7.97 1.62 2.59 2.59 0.71 0.37 0.36
TMEM163 ENST00000281924 14.01 45.63 28.01 1.62 0.73 0.82 0.71 2.01 1.27
C10orf76 ENST00000370033 14.02 29.18 19.61 1.62 1.13 1.53 0.72 1.34 0.85
CACNA2D3 ENST00000474759 14.02 13.32 11.36 1.63 2.05 2.21 0.72 0.60 0.45
TTC28 ENST00000397906 14.03 4.19 6.43 1.63 3.25 3.05 0.72 0.32 0.32
DLGAP3 ENST00000373347 14.03 2.35 5.53 1.63 3.63 3.42 0.72 0.29 0.26
HORMAD1 ENST00000361824 14.04 17.01 13.12 1.63 1.62 2.09 0.72 0.73 0.52
NASP ENST00000350030 14.04 10.52 9.79 1.63 2.19 2.29 0.72 0.50 0.40
NUP54 ENST00000264883 14.05 21.59 15.67 1.63 1.44 1.76 0.72 0.81 0.67
CDC42SE2 ENST00000505065 14.05 31.27 20.82 1.63 0.99 1.46 0.72 1.38 0.88
C7orf41 ENST00000324453 14.06 49.69 30.07 1.63 0.66 0.81 0.72 2.02 1.46
SH3KBP1 ENST00000397821 14.06 5.83 7.29 1.63 2.86 2.81 0.71 0.35 0.34
MOB3B ENST00000262244 14.07 57.11 33.76 1.63 0.56 0.89 0.71 1.50 1.73
HCN4 ENST00000261917 14.07 5.93 7.39 1.63 2.83 2.80 0.71 0.35 0.34

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.