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
CCDC94 ENST00000262962 43.65 59.37 50.54 0.76 0.51 0.67 1.78 1.41 1.86
SEMA3C ENST00000265361 43.65 26.73 33.36 0.76 1.21 0.87 1.78 1.12 1.72
CEP63 ENST00000337090 43.66 69.07 56.10 0.76 0.56 0.49 1.78 1.14 1.77
CTC-435M10.3 ENST00000540732 43.67 55.15 48.28 0.76 0.57 0.67 1.78 1.61 1.88
ARHGEF40 ENST00000298694 43.67 25.03 32.54 0.76 1.33 0.89 1.78 1.05 1.61
RNF219 ENST00000282003 43.68 47.23 43.79 0.76 0.66 0.61 1.78 2.00 2.01
PMPCB ENST00000249269 43.68 50.87 45.97 0.76 0.63 0.70 1.78 1.92 1.98
DISP1 ENST00000284476 43.69 30.18 35.08 0.76 1.10 0.86 1.78 1.41 1.75
CCRN4L ENST00000280614 43.69 36.71 38.48 0.76 0.77 0.84 1.78 1.67 2.05
STX5 ENST00000294179 43.70 19.32 29.68 0.76 1.47 0.85 1.78 0.75 1.41
IKBKAP ENST00000374647 43.70 38.25 39.35 0.76 0.76 0.78 1.78 1.70 2.04
FAM174A ENST00000312637 43.71 89.79 68.77 0.76 0.27 0.46 1.79 0.37 1.06
SLC16A9 ENST00000395348 43.71 35.45 37.80 0.76 0.77 0.84 1.79 1.56 2.01
CRTC3 ENST00000268184 43.72 15.98 28.03 0.76 1.86 0.82 1.79 0.68 1.27
CCDC104 ENST00000349456 43.72 42.67 41.42 0.76 0.61 0.73 1.79 1.90 2.02
MED10 ENST00000255764 43.73 59.39 50.58 0.76 0.51 0.66 1.79 1.41 1.86
DNAJC16 ENST00000375847 43.73 41.97 41.06 0.76 0.61 0.75 1.79 1.83 2.06
PTPN23 ENST00000265562 43.74 14.78 27.39 0.75 1.96 0.96 1.79 0.62 1.27
SLN ENST00000531293 43.74 93.64 71.11 0.75 0.28 0.43 1.78 0.28 0.86
SNAI1 ENST00000244050 43.75 35.60 37.91 0.75 0.77 0.85 1.78 1.58 2.01
C17orf49 ENST00000546495 43.75 52.46 46.83 0.75 0.65 0.67 1.78 1.84 1.88
TPP1 ENST00000299427 43.76 42.27 41.23 0.75 0.61 0.76 1.78 1.89 2.01
TMEM256-PLSCR3 ENST00000535512 43.76 43.62 41.93 0.75 0.62 0.68 1.78 1.95 2.01
KDELC2 ENST00000323468 43.77 64.18 53.39 0.75 0.49 0.62 1.78 1.21 1.84
TBC1D32 ENST00000398212 43.77 48.46 44.69 0.75 0.63 0.62 1.78 2.02 2.06

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.