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
AMY1A ENST00000370083 88.20 90.91 92.24 0.20 0.25 0.14 0.35 0.35 0.16
SLC35G5 ENST00000382435 88.20 97.64 95.72 0.20 0.21 0.07 0.34 0.19 0.11
LRTOMT ENST00000435085 88.21 67.89 81.40 0.20 0.52 0.37 0.34 1.17 0.48
CSN2 ENST00000353151 88.21 73.92 84.38 0.20 0.53 0.33 0.34 1.02 0.40
PGA5 ENST00000312403 88.22 95.94 94.83 0.20 0.22 0.09 0.34 0.20 0.11
RBFOX3 ENST00000415831 88.22 3.90 44.65 0.20 3.28 0.62 0.34 0.31 2.06
KRTAP19-4 ENST00000334058 88.23 98.09 96.77 0.22 0.20 0.08 0.34 0.16 0.08
PRDM7 ENST00000449207 88.23 75.41 85.19 0.22 0.46 0.34 0.34 0.90 0.37
WDR27 ENST00000448612 88.24 48.80 70.87 0.22 0.63 0.43 0.34 2.02 0.86
MORN1 ENST00000378531 88.24 57.73 76.00 0.22 0.57 0.38 0.34 1.46 0.62
OR2A42 ENST00000391496 88.25 83.73 89.11 0.20 0.27 0.19 0.34 0.47 0.26
KDM4E ENST00000450979 88.25 71.67 83.32 0.20 0.52 0.32 0.35 1.07 0.40
MRGPRE ENST00000436689 88.26 99.31 96.34 0.20 0.16 0.07 0.35 0.12 0.09
CYLC1 ENST00000329312 88.27 16.97 51.77 0.20 1.64 0.62 0.35 0.73 1.93
ARSF ENST00000381127 88.27 79.76 87.19 0.20 0.37 0.28 0.35 0.64 0.31
TPTE ENST00000361285 88.28 77.52 86.14 0.20 0.42 0.33 0.35 0.79 0.33
PCDHB13 ENST00000341948 88.28 87.43 90.90 0.20 0.23 0.15 0.35 0.40 0.20
CEACAM8 ENST00000244336 88.29 66.86 80.89 0.20 0.53 0.39 0.35 1.24 0.51
ETV2 ENST00000402764 88.29 73.70 84.32 0.20 0.52 0.33 0.35 1.02 0.41
NXNL2 ENST00000375854 88.30 42.85 67.38 0.20 0.62 0.52 0.35 1.92 1.15
TMEM99 ENST00000301665 88.30 97.87 95.87 0.20 0.21 0.07 0.35 0.17 0.11
ZNF697 ENST00000421812 88.31 49.72 71.55 0.20 0.66 0.44 0.35 2.02 0.83
AC004076.9 ENST00000596831 88.31 78.10 86.39 0.20 0.43 0.32 0.35 0.74 0.33
SYT8 ENST00000381968 88.32 94.61 94.21 0.20 0.23 0.09 0.35 0.24 0.12
C5orf45 ENST00000292586 88.32 72.23 83.67 0.20 0.51 0.34 0.35 1.04 0.40

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.