GeVIR Banner
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
OR2M3 ENST00000456743 97.30 97.77 99.27 0.10 0.21 0.11 0.11 0.17 0.04
DEFB135 ENST00000382208 96.12 97.46 98.83 0.11 0.22 0.10 0.11 0.19 0.05
UGT2A3 ENST00000251566 97.90 81.56 92.43 0.11 0.33 0.14 0.11 0.52 0.15
CLC ENST00000221804 96.72 89.21 95.74 0.11 0.27 0.07 0.11 0.36 0.11
COLCA1 ENST00000532918 98.49 97.87 99.59 0.10 0.21 0.12 0.11 0.17 0.05
GCNT6 ENST00000417671 97.31 56.61 80.29 0.10 0.53 0.38 0.11 1.55 0.52
PRAMEF6 ENST00000376189 96.13 97.47 98.83 0.11 0.22 0.10 0.11 0.19 0.05
FLG ENST00000368799 97.90 97.00 99.21 0.11 0.24 0.11 0.11 0.19 0.04
ODF4 ENST00000328248 96.72 73.34 88.18 0.11 0.54 0.23 0.11 1.02 0.30
ZNF560 ENST00000301480 98.50 61.60 83.41 0.10 0.54 0.33 0.11 1.41 0.40
KLRC3 ENST00000381903 97.31 86.43 94.58 0.10 0.24 0.09 0.11 0.42 0.11
KRTAP13-1 ENST00000355459 96.13 98.88 99.29 0.11 0.17 0.11 0.11 0.14 0.04
KIAA1462 ENST00000375377 96.73 25.77 62.00 0.11 1.23 0.49 0.11 1.05 1.45
CFHR1 ENST00000320493 97.91 79.67 91.63 0.11 0.37 0.14 0.11 0.65 0.18
L1TD1 ENST00000498273 96.14 73.29 87.81 0.11 0.56 0.24 0.11 1.02 0.32
PRNT ENST00000326539 97.32 97.61 99.72 0.10 0.22 0.12 0.11 0.20 0.04
GIMAP6 ENST00000328902 98.50 77.04 90.84 0.10 0.42 0.15 0.11 0.78 0.20
C5orf20 ENST00000503143 96.73 99.93 99.63 0.11 0.17 0.12 0.11 0.10 0.04
ZNF136 ENST00000343979 97.91 68.74 86.52 0.11 0.53 0.30 0.11 1.17 0.33
CST5 ENST00000304710 96.14 92.92 97.23 0.11 0.29 0.08 0.11 0.30 0.06
PTPRCAP ENST00000326294 97.32 69.42 86.57 0.10 0.56 0.30 0.11 1.13 0.33
GZMH ENST00000216338 98.51 88.90 96.48 0.10 0.25 0.07 0.11 0.35 0.08
LRRC37A3 ENST00000584306 96.74 42.94 72.51 0.11 0.63 0.44 0.11 1.90 0.83
EBLN2 ENST00000533473 96.15 97.63 98.91 0.11 0.22 0.10 0.11 0.20 0.04
SPATA3 ENST00000452881 97.92 83.65 93.54 0.11 0.27 0.13 0.11 0.47 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.