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
DCAF4L2 ENST00000319675 86.66 99.61 95.90 0.24 0.16 0.07 0.41 0.12 0.10
AC015989.2 ENST00000593319 93.51 99.61 97.88 0.13 0.16 0.09 0.14 0.12 0.04
RP11-89N17.1 ENST00000311067 93.50 99.60 97.16 0.13 0.16 0.08 0.14 0.12 0.07
SBP1 ENST00000594414 96.41 99.60 99.20 0.10 0.16 0.11 0.11 0.12 0.04
F8A1 ENST00000369446 71.56 99.59 88.75 0.38 0.16 0.20 0.82 0.12 0.28
AC020907.1 ENST00000313865 83.20 99.59 94.00 0.28 0.16 0.09 0.54 0.12 0.11
FOXD4L6 ENST00000377473 93.47 99.58 96.63 0.13 0.16 0.08 0.15 0.12 0.08
MRGPRX1 ENST00000302797 96.36 99.58 99.49 0.10 0.16 0.11 0.11 0.12 0.05
AL583828.1 ENST00000558378 97.88 99.57 99.52 0.11 0.16 0.12 0.11 0.12 0.05
CXorf67 ENST00000342995 99.08 99.57 99.72 0.11 0.16 0.12 0.12 0.12 0.04
AC005477.1 ENST00000542853 93.42 99.56 98.50 0.13 0.16 0.10 0.15 0.12 0.05
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
TAS2R10 ENST00000240619 88.56 99.55 96.89 0.20 0.16 0.08 0.34 0.13 0.07
AC008132.13 ENST00000342005 93.39 99.55 97.57 0.13 0.16 0.09 0.15 0.13 0.06
SRY ENST00000383070 93.37 99.54 97.44 0.15 0.16 0.08 0.15 0.13 0.07
AC074389.6 ENST00000382528 97.95 99.54 99.80 0.11 0.16 0.12 0.11 0.13 0.04
AP001885.1 ENST00000444002 93.36 99.53 96.72 0.15 0.16 0.08 0.15 0.13 0.08
OR7E24 ENST00000456448 96.81 99.52 99.11 0.09 0.16 0.11 0.11 0.13 0.04
TAS2R16 ENST00000249284 88.84 99.52 96.98 0.19 0.16 0.08 0.32 0.13 0.07
HEPN1 ENST00000408930 87.35 99.51 96.20 0.23 0.16 0.07 0.38 0.13 0.10
PRR21 ENST00000408934 89.40 99.51 96.50 0.16 0.16 0.07 0.32 0.13 0.07
SPRR2A ENST00000392653 84.40 99.50 94.73 0.30 0.16 0.09 0.46 0.13 0.11
C10orf111 ENST00000378207 98.82 99.50 99.93 0.10 0.16 0.12 0.11 0.13 0.04
BLID ENST00000560104 96.18 99.49 99.43 0.11 0.16 0.11 0.11 0.13 0.05
ZNF497 ENST00000311044 94.83 99.49 99.09 0.10 0.16 0.11 0.11 0.13 0.04

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.