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
ZFYVE28 ENST00000290974 54.88 22.26 36.73 0.63 1.53 0.82 1.71 0.82 1.94
ABCC3 ENST00000285238 54.89 49.29 51.15 0.63 0.65 0.65 1.71 2.02 1.90
SLC45A4 ENST00000024061 54.89 36.94 44.42 0.63 0.75 0.61 1.71 1.70 2.04
FAM196A ENST00000522781 54.90 16.35 33.79 0.63 1.78 0.89 1.70 0.69 1.74
BSCL2 ENST00000433053 54.90 56.02 55.03 0.63 0.49 0.51 1.70 1.56 1.73
THSD1 ENST00000258613 54.91 46.40 49.58 0.63 0.73 0.67 1.70 2.04 1.84
CLIC5 ENST00000185206 54.91 67.05 61.70 0.63 0.54 0.46 1.70 1.24 1.46
IGDCC4 ENST00000352385 54.92 29.07 40.25 0.63 1.13 0.81 1.70 1.32 2.00
KRT12 ENST00000251643 54.92 71.00 64.25 0.63 0.49 0.51 1.70 1.07 1.35
SNTB1 ENST00000395601 54.93 35.74 43.71 0.63 0.78 0.61 1.70 1.58 2.01
HYAL1 ENST00000266031 54.94 57.27 55.79 0.63 0.56 0.52 1.70 1.49 1.73
LRRC40 ENST00000370952 54.94 77.24 68.04 0.63 0.43 0.51 1.70 0.78 1.10
COL6A3 ENST00000295550 54.95 28.39 40.02 0.63 1.16 0.82 1.70 1.22 1.99
ESRRA ENST00000405666 54.95 25.36 38.44 0.63 1.27 0.84 1.70 1.03 2.04
PSMB9 ENST00000374859 54.96 58.20 56.35 0.63 0.54 0.49 1.70 1.44 1.75
RBAK-RBAKDN ENST00000396904 54.96 42.73 47.65 0.63 0.62 0.65 1.70 1.92 1.88
GNG10 ENST00000374293 54.97 96.44 79.00 0.63 0.22 0.39 1.69 0.19 0.53
CERS3 ENST00000284382 54.97 31.98 41.71 0.63 0.92 0.72 1.68 1.48 2.01
TXNDC16 ENST00000281741 54.98 33.35 42.40 0.62 0.85 0.68 1.68 1.51 2.01
EVI2B ENST00000330927 54.98 39.06 45.71 0.62 0.70 0.67 1.68 1.63 1.99
SSMEM1 ENST00000297819 54.99 96.15 78.78 0.62 0.21 0.39 1.69 0.20 0.52
SYDE2 ENST00000341460 54.99 54.90 54.50 0.62 0.57 0.57 1.68 1.62 1.75
RSPH4A ENST00000229554 55.00 50.59 52.00 0.62 0.63 0.62 1.68 1.94 1.93
RASSF1 ENST00000357043 55.00 69.09 63.14 0.62 0.56 0.49 1.68 1.14 1.38
CEP57L1 ENST00000407272 55.01 51.60 52.60 0.62 0.62 0.61 1.69 1.87 1.89

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.