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
FIG4 ENST00000230124 29.57 68.00 47.58 1.06 0.52 0.65 1.54 1.19 1.89
HCRTR2 ENST00000370862 29.58 33.44 29.69 1.06 0.84 0.86 1.54 1.52 1.41
KCNC3 ENST00000477616 29.59 29.41 27.64 1.06 1.10 0.96 1.53 1.38 1.27
CPVL ENST00000409850 29.59 59.28 42.78 1.06 0.49 0.70 1.53 1.42 2.02
ALDOA ENST00000395248 29.60 37.51 31.78 1.06 0.78 0.89 1.53 1.67 1.58
SLC45A3 ENST00000367145 29.60 45.84 35.81 1.06 0.73 0.85 1.53 2.01 1.79
PKNOX1 ENST00000291547 29.61 10.25 17.82 1.06 2.29 1.67 1.53 0.49 0.78
WLS ENST00000354777 29.61 28.16 27.06 1.06 1.18 0.99 1.53 1.21 1.27
NANOS3 ENST00000339133 29.62 64.67 45.86 1.06 0.48 0.68 1.53 1.24 1.97
RPL36AL ENST00000298289 29.62 85.43 57.45 1.06 0.25 0.51 1.53 0.45 1.66
FKBP2 ENST00000394540 29.63 51.24 38.69 1.06 0.65 0.82 1.53 1.90 2.02
GYS1 ENST00000323798 29.63 27.48 26.71 1.06 1.25 1.00 1.54 1.16 1.27
ATP6V1B1 ENST00000234396 29.64 50.80 38.49 1.06 0.63 0.84 1.54 1.93 2.05
NPY2R ENST00000329476 29.64 47.62 36.83 1.06 0.62 0.81 1.54 1.97 1.94
HOXD10 ENST00000249501 29.65 42.00 34.00 1.06 0.59 0.89 1.55 1.84 1.72
NFX1 ENST00000379540 29.65 22.38 24.04 1.06 1.51 1.10 1.55 0.82 1.06
PITX1 ENST00000265340 29.66 19.36 22.67 1.06 1.49 1.18 1.56 0.74 0.97
SLC35G2 ENST00000446465 29.66 45.04 35.51 1.06 0.67 0.85 1.56 1.97 1.78
SLC22A17 ENST00000397267 29.67 35.43 30.80 1.06 0.77 0.78 1.56 1.56 1.49
USP4 ENST00000265560 29.67 33.44 29.71 1.06 0.84 0.86 1.56 1.51 1.41
ATAD2 ENST00000287394 29.68 8.51 16.95 1.06 2.52 1.67 1.56 0.46 0.71
LACTB ENST00000261893 29.68 55.08 40.58 1.06 0.58 0.81 1.56 1.63 2.04
STC2 ENST00000265087 29.69 26.47 26.25 1.06 1.18 1.01 1.57 1.10 1.26
CD53 ENST00000271324 29.69 55.17 40.63 1.06 0.57 0.81 1.57 1.61 2.05
ATG14 ENST00000247178 29.70 25.55 25.71 1.08 1.25 1.05 1.57 1.05 1.22

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.