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
SLC12A8 ENST00000393469 64.57 67.93 68.24 0.56 0.52 0.52 1.18 1.17 1.08
PRX ENST00000324001 64.57 52.19 58.44 0.56 0.62 0.52 1.18 1.84 1.65
TRIM15 ENST00000376694 64.58 67.37 67.88 0.56 0.56 0.51 1.18 1.21 1.12
CALHM2 ENST00000260743 64.58 83.80 77.38 0.56 0.27 0.35 1.18 0.47 0.58
TRIP6 ENST00000200457 64.59 38.22 50.44 0.56 0.76 0.67 1.18 1.70 1.88
SNAPC1 ENST00000216294 64.59 79.28 74.84 0.56 0.38 0.39 1.18 0.67 0.64
RGS12 ENST00000344733 64.60 31.05 46.48 0.56 1.04 0.67 1.18 1.35 1.91
HIST1H3E ENST00000360408 64.60 97.10 84.12 0.56 0.24 0.34 1.18 0.18 0.42
GAS6 ENST00000327773 64.61 25.04 43.16 0.56 1.33 0.65 1.19 1.04 1.99
EPDR1 ENST00000199448 64.61 60.15 63.56 0.56 0.52 0.49 1.19 1.39 1.39
NPVF ENST00000222674 64.62 88.31 79.78 0.54 0.23 0.38 1.19 0.37 0.53
NOB1 ENST00000268802 64.62 66.79 67.52 0.54 0.56 0.51 1.19 1.23 1.13
HSPA12B ENST00000254963 64.63 33.30 47.82 0.54 0.84 0.65 1.19 1.51 1.89
KISS1R ENST00000234371 64.64 23.98 42.57 0.54 1.37 0.68 1.19 0.95 2.02
ZNF235 ENST00000291182 64.64 56.20 61.02 0.54 0.52 0.43 1.19 1.55 1.56
IKBIP ENST00000299157 64.65 72.13 70.73 0.54 0.52 0.43 1.19 1.04 0.86
SHCBP1L ENST00000367547 64.65 71.32 70.23 0.54 0.53 0.43 1.19 1.07 0.91
MFAP5 ENST00000359478 64.66 46.29 55.05 0.54 0.73 0.51 1.19 2.04 1.74
LIPA ENST00000336233 64.66 57.08 61.59 0.54 0.56 0.46 1.19 1.51 1.48
KCNK6 ENST00000263372 64.67 72.66 71.12 0.54 0.47 0.43 1.19 1.04 0.86
TMEM126A ENST00000304511 64.67 72.38 70.88 0.54 0.51 0.43 1.19 1.03 0.86
CCNF ENST00000397066 64.68 20.66 40.87 0.54 1.47 0.80 1.19 0.78 2.06
N6AMT1 ENST00000303775 64.68 81.46 76.10 0.54 0.33 0.38 1.18 0.55 0.62
TRIM11 ENST00000284551 64.69 18.28 39.83 0.54 1.49 0.78 1.18 0.74 2.03
MDH1B ENST00000374412 64.69 64.87 66.44 0.54 0.48 0.51 1.18 1.24 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.