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
TRAPPC8 ENST00000283351 31.12 2.63 14.62 0.95 3.55 1.97 1.68 0.29 0.59
ZNF106 ENST00000263805 31.13 18.56 23.01 0.96 1.49 1.20 1.68 0.76 0.98
CUTC ENST00000370476 31.13 44.78 36.07 0.96 0.67 0.87 1.68 1.97 1.79
PPFIBP1 ENST00000318304 31.14 36.29 31.90 0.96 0.82 0.91 1.69 1.60 1.57
SFMBT2 ENST00000361972 31.15 8.75 17.84 0.96 2.48 1.66 1.69 0.48 0.77
MCTP1 ENST00000515393 31.15 24.84 26.17 0.96 1.33 0.99 1.70 1.06 1.25
RBMX2 ENST00000305536 31.16 14.70 21.06 0.96 1.99 1.42 1.70 0.62 0.89
UNC119B ENST00000344651 31.16 24.80 26.14 0.96 1.33 0.99 1.70 1.05 1.27
CERS5 ENST00000317551 31.17 52.46 40.10 0.96 0.66 0.82 1.70 1.84 1.99
EXOSC2 ENST00000372358 31.17 60.69 44.43 0.96 0.54 0.61 1.70 1.40 2.04
ANGEL2 ENST00000366962 31.18 37.18 32.37 0.96 0.78 0.91 1.69 1.67 1.61
HERPUD1 ENST00000439977 31.18 8.14 17.53 0.96 2.53 1.63 1.69 0.44 0.75
ALPL ENST00000374840 31.19 36.60 32.08 0.96 0.78 0.90 1.69 1.64 1.60
FAM110B ENST00000361488 31.19 36.43 32.03 0.96 0.82 0.90 1.69 1.64 1.60
CAPN1 ENST00000527323 31.20 38.81 33.16 0.96 0.70 0.87 1.69 1.66 1.70
ITGA4 ENST00000397033 31.20 23.72 25.57 0.96 1.39 1.05 1.69 0.93 1.19
SLC6A12 ENST00000428720 31.21 47.63 37.66 0.96 0.62 0.82 1.69 1.97 2.01
VTCN1 ENST00000369458 31.21 91.29 61.98 0.97 0.23 0.49 1.68 0.34 1.46
MAP4K2 ENST00000294066 31.22 37.36 32.49 0.97 0.76 0.89 1.68 1.65 1.63
GDF5OS ENST00000374375 31.22 67.60 48.27 0.97 0.53 0.67 1.68 1.19 1.88
SNX24 ENST00000261369 31.23 68.48 48.76 0.97 0.53 0.68 1.68 1.20 1.85
HSCB ENST00000216027 31.23 49.27 38.54 0.97 0.65 0.84 1.68 2.03 2.02
LMO1 ENST00000335790 31.24 32.83 30.23 0.97 0.85 0.81 1.68 1.44 1.44
RLBP1 ENST00000268125 31.24 58.36 43.17 0.97 0.54 0.65 1.68 1.41 1.99
GSS ENST00000216951 31.25 42.95 35.31 0.96 0.63 0.87 1.68 1.90 1.75

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.