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
CAPNS2 ENST00000457326 53.46 75.28 66.00 0.62 0.49 0.51 1.76 0.90 1.22
OR5B21 ENST00000360374 53.47 96.09 77.97 0.62 0.21 0.38 1.77 0.20 0.54
NSUN2 ENST00000264670 53.47 26.26 38.16 0.62 1.19 0.85 1.77 1.08 2.05
FOCAD ENST00000380249 53.48 45.92 48.60 0.62 0.76 0.67 1.77 2.02 1.85
TBX6 ENST00000395224 53.48 39.62 45.25 0.62 0.68 0.70 1.77 1.65 2.00
LRAT ENST00000336356 53.49 74.63 65.65 0.62 0.54 0.51 1.76 0.98 1.29
RAB20 ENST00000267328 53.49 82.74 70.42 0.62 0.33 0.43 1.76 0.50 0.91
ASAP3 ENST00000336689 53.50 36.26 43.23 0.62 0.82 0.65 1.76 1.61 1.99
MTERFD3 ENST00000552029 53.50 70.85 63.29 0.62 0.49 0.49 1.76 1.07 1.36
PDCD6 ENST00000264933 53.51 50.57 51.12 0.62 0.63 0.65 1.76 1.95 1.89
GNA14 ENST00000341700 53.51 86.27 72.57 0.62 0.25 0.46 1.76 0.42 0.82
POLR3G ENST00000399107 53.52 87.43 73.23 0.62 0.23 0.43 1.76 0.40 0.79
PLD2 ENST00000263088 53.53 61.25 57.28 0.62 0.53 0.51 1.76 1.40 1.69
SPATA20 ENST00000006658 53.53 37.01 43.62 0.62 0.77 0.59 1.76 1.68 2.01
CCND1 ENST00000227507 53.54 18.82 34.43 0.62 1.53 0.90 1.76 0.74 1.76
TPPP ENST00000360578 53.54 50.92 51.34 0.62 0.63 0.63 1.76 1.94 1.91
TNFRSF25 ENST00000377782 53.55 27.90 39.07 0.62 1.20 0.78 1.76 1.18 2.06
PGBD1 ENST00000405948 53.55 47.74 49.57 0.62 0.59 0.67 1.76 1.99 1.85
ZFAND4 ENST00000344646 53.56 57.45 55.10 0.62 0.56 0.51 1.76 1.49 1.73
ATPIF1 ENST00000335514 53.56 87.11 73.06 0.62 0.22 0.42 1.75 0.41 0.80
IGSF22 ENST00000513874 53.57 70.30 62.97 0.62 0.52 0.51 1.75 1.10 1.39
C15orf39 ENST00000360639 53.57 28.00 39.15 0.62 1.20 0.77 1.75 1.18 2.06
WDR78 ENST00000371026 53.58 53.25 52.75 0.62 0.66 0.61 1.75 1.73 1.88
TRIM10 ENST00000449742 53.58 58.31 55.63 0.62 0.54 0.53 1.75 1.43 1.73
KRT71 ENST00000267119 53.59 52.01 51.99 0.62 0.61 0.62 1.75 1.86 1.93

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.