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
WDR12 ENST00000261015 32.03 32.81 30.66 0.96 0.84 0.80 1.72 1.44 1.48
PUS10 ENST00000316752 32.03 56.52 42.56 0.96 0.52 0.68 1.72 1.54 2.01
BUB1 ENST00000302759 32.04 31.83 30.13 0.96 0.94 0.81 1.72 1.48 1.46
EPHB6 ENST00000392957 32.04 32.37 30.41 0.97 0.87 0.80 1.72 1.46 1.46
AKAP11 ENST00000025301 32.05 11.88 19.99 0.97 2.10 1.47 1.72 0.58 0.85
COG4 ENST00000323786 32.05 38.43 33.40 0.97 0.75 0.87 1.72 1.70 1.72
SLC48A1 ENST00000442218 32.06 39.41 33.90 0.97 0.70 0.89 1.72 1.63 1.73
UQCRC2 ENST00000268379 32.06 44.58 36.41 0.97 0.65 0.84 1.72 1.97 1.87
NELL1 ENST00000357134 32.07 39.82 34.13 0.97 0.65 0.89 1.72 1.68 1.75
PDZD4 ENST00000164640 32.07 18.06 23.17 0.97 1.53 1.19 1.72 0.74 1.02
UHRF1BP1L ENST00000279907 32.08 17.37 22.88 0.97 1.59 1.19 1.72 0.75 0.97
C15orf59 ENST00000569673 32.09 45.00 36.73 0.97 0.68 0.82 1.72 1.97 1.94
TMEM243 ENST00000433078 32.09 94.16 64.41 0.97 0.25 0.51 1.72 0.25 1.34
HADHA ENST00000380649 32.10 32.09 30.28 0.96 0.91 0.84 1.72 1.46 1.44
ITGB1BP1 ENST00000360635 32.10 56.57 42.58 0.96 0.53 0.67 1.72 1.55 2.02
CXorf23 ENST00000379687 32.11 19.85 24.02 0.96 1.42 1.10 1.72 0.74 1.06
POMGNT2 ENST00000344697 32.11 57.38 43.12 0.96 0.54 0.65 1.72 1.49 1.99
RNFT1 ENST00000305783 32.12 54.21 41.38 0.96 0.62 0.73 1.72 1.70 2.03
STX7 ENST00000367941 32.12 55.54 42.04 0.97 0.56 0.70 1.72 1.60 1.98
ABHD5 ENST00000458276 32.13 56.03 42.34 0.97 0.49 0.70 1.72 1.56 2.02
ALG6 ENST00000371108 32.13 29.54 29.01 0.97 1.10 0.82 1.72 1.39 1.31
NNAT ENST00000062104 32.14 62.41 45.95 0.97 0.52 0.70 1.72 1.32 1.97
GALNT3 ENST00000392701 32.14 47.20 37.93 0.97 0.66 0.85 1.72 2.01 2.02
LMBR1L ENST00000267102 32.15 58.44 43.63 0.97 0.54 0.59 1.72 1.38 2.02
SMPX ENST00000379494 32.15 50.25 39.53 0.96 0.67 0.80 1.72 1.99 2.03

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.