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
FAM117A ENST00000240364 24.15 49.59 35.04 1.34 0.66 0.87 1.12 2.02 1.75
NAA60 ENST00000407558 24.16 33.17 26.81 1.34 0.82 0.96 1.12 1.51 1.28
NAA60 ENST00000608722 24.16 33.19 26.84 1.34 0.82 0.97 1.12 1.50 1.27
PAX1 ENST00000398485 24.17 25.00 22.74 1.34 1.33 1.18 1.12 1.05 0.98
GPR3 ENST00000374024 24.17 80.69 51.58 1.34 0.37 0.62 1.12 0.57 1.94
GPC4 ENST00000370828 24.18 15.90 17.96 1.34 1.89 1.71 1.12 0.68 0.78
ABCB4 ENST00000265723 24.18 24.76 22.62 1.34 1.32 1.18 1.13 1.05 0.96
BSN ENST00000296452 24.19 4.45 11.93 1.35 3.27 2.28 1.13 0.32 0.46
ADRA2C ENST00000330055 24.19 30.93 25.63 1.35 1.05 1.06 1.13 1.36 1.20
CADM3 ENST00000368124 24.20 11.98 15.92 1.35 2.07 1.76 1.13 0.58 0.66
PDE4A ENST00000352831 24.20 11.35 15.61 1.35 2.10 1.77 1.12 0.56 0.66
SEL1L3 ENST00000399878 24.21 17.19 18.70 1.35 1.61 1.57 1.12 0.75 0.81
AKAP10 ENST00000225737 24.21 21.21 20.85 1.35 1.44 1.47 1.12 0.81 0.87
OXR1 ENST00000442977 24.22 14.89 17.43 1.35 1.94 1.62 1.12 0.62 0.75
FAM214A ENST00000261844 24.22 14.96 17.46 1.35 1.92 1.62 1.12 0.63 0.75
CLMP ENST00000448775 24.23 55.45 38.10 1.35 0.58 0.86 1.12 1.60 2.02
CCNG1 ENST00000340828 24.23 48.38 34.53 1.35 0.63 0.90 1.12 2.00 1.77
AHDC1 ENST00000374011 24.24 0.48 9.90 1.35 4.11 2.30 1.12 0.28 0.41
TWF1 ENST00000548315 24.24 42.78 31.70 1.35 0.63 0.89 1.12 1.91 1.58
HSPH1 ENST00000320027 24.25 8.12 13.86 1.35 2.53 2.10 1.12 0.44 0.59
MRPL13 ENST00000306185 24.25 81.02 51.79 1.35 0.35 0.62 1.12 0.55 1.93
FAM46D ENST00000538312 24.26 25.42 23.03 1.35 1.25 1.20 1.12 1.05 0.98
LAMC2 ENST00000264144 24.27 33.39 26.98 1.35 0.85 1.00 1.12 1.50 1.28
PTN ENST00000348225 24.27 53.24 36.97 1.35 0.66 0.78 1.12 1.74 1.95
PLCL1 ENST00000428675 24.28 23.61 22.05 1.35 1.39 1.15 1.12 0.93 0.96

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.