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
ZNF253 ENST00000589717 89.10 84.34 89.84 0.19 0.29 0.18 0.32 0.44 0.23
NOL3 ENST00000568146 89.11 83.72 89.54 0.19 0.27 0.18 0.32 0.47 0.23
MAGEA11 ENST00000355220 89.11 41.48 67.03 0.19 0.62 0.52 0.32 1.82 1.17
R3HCC1 ENST00000265806 89.12 73.32 84.56 0.19 0.56 0.34 0.32 1.02 0.40
SULT2A1 ENST00000222002 89.12 90.05 92.27 0.19 0.25 0.14 0.32 0.37 0.15
CEACAM19 ENST00000403660 89.13 81.82 88.60 0.19 0.35 0.22 0.32 0.51 0.28
GP1BB ENST00000366425 89.13 73.39 84.61 0.19 0.54 0.34 0.32 1.03 0.40
GOLGA8I ENST00000450802 89.14 84.48 89.90 0.19 0.29 0.18 0.32 0.44 0.23
RP11-1396O13.13 ENST00000508324 89.14 90.99 92.82 0.19 0.25 0.14 0.32 0.35 0.15
GPR78 ENST00000382487 89.15 89.95 92.25 0.19 0.25 0.14 0.32 0.37 0.16
FAM86B2 ENST00000262365 89.15 85.99 90.65 0.19 0.27 0.15 0.32 0.43 0.20
AP003062.1 ENST00000597621 89.16 99.66 97.18 0.19 0.17 0.08 0.32 0.12 0.06
C3orf65 ENST00000296270 89.16 86.26 90.79 0.18 0.25 0.15 0.32 0.42 0.20
C3orf79 ENST00000446603 89.17 74.31 85.09 0.18 0.53 0.33 0.32 1.01 0.38
CASP5 ENST00000393141 89.17 81.31 88.39 0.18 0.33 0.22 0.32 0.54 0.30
XG ENST00000419513 89.18 84.53 89.91 0.18 0.29 0.18 0.32 0.42 0.23
AC010441.1 ENST00000600109 89.18 96.41 95.56 0.18 0.22 0.08 0.32 0.19 0.11
GPR32 ENST00000270590 89.19 97.98 96.38 0.18 0.20 0.07 0.32 0.17 0.09
SLC22A24 ENST00000417740 89.19 79.25 87.38 0.18 0.38 0.28 0.32 0.67 0.31
C2orf73 ENST00000398634 89.20 85.15 90.21 0.18 0.25 0.18 0.32 0.45 0.21
HHLA3 ENST00000370940 89.21 90.56 92.63 0.18 0.25 0.14 0.32 0.37 0.15
CDH26 ENST00000348616 89.21 68.48 82.22 0.18 0.53 0.35 0.32 1.20 0.44
UGT2B17 ENST00000317746 89.22 56.31 75.78 0.18 0.52 0.38 0.32 1.55 0.63
DEFB115 ENST00000400552 89.22 96.78 95.78 0.18 0.23 0.07 0.32 0.19 0.11
GOLGA8J ENST00000567927 89.23 92.38 93.56 0.18 0.25 0.13 0.32 0.30 0.15

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.