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
IKBKG ENST00000369609 75.03 75.92 78.71 0.38 0.43 0.38 0.77 0.87 0.54
C1orf116 ENST00000359470 75.03 38.21 56.44 0.38 0.77 0.52 0.77 1.70 1.70
TUSC5 ENST00000333813 75.04 87.11 84.39 0.38 0.22 0.33 0.77 0.41 0.40
TRDN ENST00000398178 75.04 52.08 64.99 0.38 0.59 0.51 0.77 1.85 1.32
DNAJC30 ENST00000395176 75.05 67.33 73.95 0.38 0.56 0.40 0.77 1.20 0.69
FRMPD2 ENST00000374201 75.05 65.73 73.15 0.38 0.53 0.43 0.77 1.22 0.79
MAB21L3 ENST00000369500 75.06 58.48 68.79 0.38 0.53 0.46 0.77 1.39 1.05
LHPP ENST00000368842 75.06 80.25 81.00 0.38 0.37 0.39 0.77 0.58 0.50
KLHL21 ENST00000377658 75.07 55.08 66.80 0.38 0.58 0.53 0.77 1.63 1.20
TBXAS1 ENST00000416849 75.07 74.77 78.15 0.38 0.54 0.39 0.77 0.96 0.55
CCZ1B ENST00000316731 75.08 72.22 76.74 0.38 0.51 0.34 0.77 1.04 0.60
LRRC47 ENST00000378251 75.08 19.49 45.99 0.38 1.46 0.68 0.77 0.74 1.97
PDK3 ENST00000441463 75.09 28.75 51.00 0.38 1.15 0.66 0.77 1.29 1.87
ANKRD33 ENST00000301190 75.09 92.07 86.75 0.38 0.24 0.30 0.77 0.32 0.32
HCAR1 ENST00000432564 75.10 80.27 81.04 0.38 0.37 0.39 0.77 0.58 0.50
ZNF546 ENST00000347077 75.10 51.87 64.90 0.38 0.59 0.51 0.77 1.87 1.33
NCCRP1 ENST00000339852 75.11 80.89 81.35 0.38 0.35 0.38 0.77 0.57 0.49
PRELID2 ENST00000334744 75.11 79.79 80.76 0.38 0.35 0.39 0.76 0.63 0.52
NAPSA ENST00000253719 75.12 84.14 82.97 0.38 0.27 0.32 0.76 0.45 0.40
TRPM5 ENST00000155858 75.13 55.30 66.95 0.38 0.57 0.53 0.76 1.61 1.19
AEN ENST00000332810 75.13 93.94 87.67 0.38 0.25 0.24 0.76 0.26 0.31
OR9A4 ENST00000548136 75.14 94.63 88.04 0.38 0.23 0.23 0.76 0.24 0.31
TAS2R4 ENST00000247881 75.14 94.07 87.76 0.38 0.25 0.24 0.76 0.26 0.32
CHST5 ENST00000336257 75.15 63.77 72.07 0.38 0.49 0.43 0.76 1.22 0.81
ADARB2 ENST00000381312 75.15 17.44 44.95 0.38 1.59 0.68 0.76 0.74 2.04

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.