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
IFT52 ENST00000373030 31.75 45.76 36.97 0.96 0.75 0.78 1.71 2.02 1.94
CYB561A3 ENST00000426130 33.19 49.67 39.79 0.91 0.66 0.80 1.69 2.02 2.02
TBC1D4 ENST00000377636 33.21 49.56 39.76 0.91 0.66 0.80 1.70 2.02 2.03
KIAA0930 ENST00000251993 33.92 45.90 38.21 0.92 0.75 0.85 1.75 2.02 2.04
LINGO3 ENST00000585527 34.05 45.78 38.22 0.92 0.75 0.85 1.75 2.02 2.04
DLAT ENST00000280346 34.47 45.77 38.42 0.99 0.75 0.84 1.80 2.02 2.04
RNF13 ENST00000344229 34.74 48.43 39.94 0.95 0.63 0.81 1.80 2.02 2.01
FKTN ENST00000223528 35.10 45.99 38.86 0.92 0.77 0.80 1.85 2.02 2.05
PGAP3 ENST00000300658 35.26 48.82 40.31 0.92 0.63 0.80 1.85 2.02 2.00
NDUFV2 ENST00000318388 36.53 45.73 39.47 0.95 0.75 0.78 1.78 2.02 2.04
SUSD1 ENST00000374270 36.85 49.49 41.40 0.92 0.65 0.73 1.75 2.02 2.02
STK36 ENST00000295709 37.90 46.45 40.44 0.92 0.73 0.80 1.74 2.02 2.03
MTHFR ENST00000376592 38.36 49.65 42.23 0.90 0.66 0.70 1.73 2.02 2.01
IL12B ENST00000231228 38.41 49.67 42.30 0.90 0.66 0.70 1.73 2.02 2.01
FHL3 ENST00000373016 38.61 49.76 42.48 0.92 0.66 0.68 1.74 2.02 2.00
RNF180 ENST00000389100 39.11 46.50 41.02 0.90 0.73 0.76 1.77 2.02 2.04
UFC1 ENST00000368003 39.60 49.84 43.09 0.90 0.66 0.65 1.75 2.02 2.01
CC2D2B ENST00000410012 39.61 49.73 43.05 0.90 0.66 0.66 1.75 2.02 2.02
SLC22A15 ENST00000369503 39.99 49.80 43.25 0.86 0.66 0.65 1.76 2.02 1.99
NMD3 ENST00000460469 41.42 45.95 41.91 0.82 0.76 0.68 1.68 2.02 2.01
POC1B ENST00000313546 42.49 48.46 43.84 0.76 0.63 0.61 1.75 2.02 2.02
ABCA4 ENST00000370225 43.14 49.68 45.07 0.82 0.66 0.70 1.79 2.02 2.02
TBC1D32 ENST00000398212 43.77 48.46 44.69 0.75 0.63 0.62 1.78 2.02 2.06
MRPS22 ENST00000495075 43.95 48.43 44.77 0.75 0.63 0.65 1.77 2.02 2.05
GSTA4 ENST00000370963 43.97 48.44 44.76 0.75 0.63 0.65 1.77 2.02 2.05

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.