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
AC023632.1 ENST00000391679 93.23 99.43 98.65 0.15 0.16 0.10 0.15 0.12 0.05
C15orf65 ENST00000569691 93.24 70.90 85.25 0.15 0.49 0.34 0.15 1.07 0.36
ANKRD34C ENST00000421388 93.24 36.50 66.70 0.15 0.80 0.54 0.15 1.63 1.20
PRSS56 ENST00000449534 93.25 37.95 67.54 0.15 0.78 0.51 0.15 1.70 1.13
RP11-181C3.1 ENST00000501499 93.25 79.21 89.25 0.15 0.39 0.19 0.15 0.69 0.25
GGNBP1 ENST00000374458 93.26 40.09 68.81 0.15 0.63 0.46 0.15 1.71 1.05
C1orf229 ENST00000408893 93.26 99.46 97.28 0.15 0.16 0.08 0.15 0.13 0.07
LINC00923 ENST00000503874 93.27 79.08 89.41 0.15 0.39 0.18 0.15 0.70 0.24
CTXN1 ENST00000318978 93.28 85.57 91.59 0.15 0.27 0.15 0.15 0.44 0.18
DNAH10OS ENST00000514254 93.28 94.50 96.83 0.15 0.23 0.08 0.15 0.24 0.07
C2orf27B ENST00000303798 93.29 94.97 96.52 0.15 0.23 0.07 0.15 0.21 0.07
SHISA7 ENST00000376325 93.29 25.30 59.76 0.15 1.28 0.49 0.15 1.03 1.66
DKFZP434O1614 ENST00000554299 93.30 99.47 97.32 0.15 0.16 0.08 0.15 0.13 0.07
ANKRD20A2 ENST00000377601 93.30 96.57 97.63 0.15 0.23 0.09 0.15 0.19 0.06
MTRNR2L3 ENST00000543500 93.31 99.47 98.66 0.15 0.16 0.10 0.15 0.13 0.05
RP11-1102P16.1 ENST00000523987 93.31 92.43 95.77 0.15 0.27 0.07 0.15 0.30 0.11
HRK ENST00000257572 93.32 89.59 94.30 0.15 0.27 0.10 0.15 0.37 0.12
GJE1 ENST00000450456 93.32 70.31 85.30 0.15 0.52 0.34 0.15 1.10 0.36
FRAT2 ENST00000371019 93.33 86.49 93.12 0.15 0.24 0.14 0.15 0.42 0.15
CTD-2014B16.3 ENST00000554907 93.33 89.29 93.20 0.15 0.27 0.14 0.15 0.37 0.15
VSTM2B ENST00000335523 93.34 68.52 82.65 0.15 0.52 0.32 0.15 1.20 0.43
DEFB113 ENST00000398718 93.34 93.41 94.46 0.15 0.28 0.10 0.15 0.28 0.12
AC021218.2 ENST00000377722 93.35 83.83 91.56 0.15 0.28 0.15 0.15 0.47 0.18
RD3L ENST00000557640 93.35 59.80 79.45 0.15 0.52 0.39 0.15 1.37 0.52
AP001885.1 ENST00000444002 93.36 99.53 96.72 0.15 0.16 0.08 0.15 0.13 0.08

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.