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
ZNF280B ENST00000360412 56.30 36.04 44.78 0.58 0.80 0.65 1.63 1.58 2.04
ASB18 ENST00000409749 56.31 86.97 74.56 0.58 0.22 0.40 1.63 0.40 0.69
MPHOSPH9 ENST00000392425 56.31 32.54 42.74 0.58 0.86 0.70 1.63 1.49 2.02
CCDC19 ENST00000368099 56.32 52.94 54.13 0.58 0.63 0.59 1.63 1.78 1.75
GTF3C6 ENST00000329970 56.32 66.41 62.17 0.58 0.54 0.48 1.63 1.20 1.44
TMEM204 ENST00000566264 56.33 16.88 34.80 0.58 1.66 0.90 1.63 0.71 1.77
WSCD1 ENST00000574946 56.33 35.13 44.19 0.58 0.76 0.62 1.63 1.58 2.05
ILVBL ENST00000263383 56.34 51.84 53.49 0.58 0.59 0.63 1.63 1.87 1.82
ERN2 ENST00000256797 56.35 56.25 55.98 0.58 0.52 0.49 1.63 1.55 1.76
FBXL13 ENST00000313221 56.35 49.98 52.44 0.58 0.66 0.61 1.63 2.02 1.92
CCDC89 ENST00000316398 56.36 63.10 60.17 0.58 0.48 0.48 1.63 1.30 1.61
ORC1 ENST00000371568 56.36 46.02 50.21 0.58 0.77 0.63 1.63 2.03 1.90
ARHGEF18 ENST00000359920 56.37 22.57 37.70 0.58 1.47 0.84 1.62 0.85 2.01
IL20RB ENST00000329582 56.37 68.31 63.52 0.58 0.52 0.49 1.63 1.20 1.39
CHURC1 ENST00000607599 56.38 90.95 76.77 0.58 0.25 0.34 1.63 0.35 0.61
BRF1 ENST00000546474 56.38 28.85 40.80 0.58 1.15 0.80 1.63 1.29 2.04
AEBP1 ENST00000223357 56.39 34.89 44.07 0.58 0.76 0.61 1.63 1.55 2.02
PCNXL2 ENST00000258229 56.39 36.28 44.98 0.58 0.82 0.68 1.63 1.61 2.04
DHTKD1 ENST00000263035 56.40 70.17 64.63 0.58 0.53 0.51 1.63 1.12 1.32
STMN3 ENST00000370053 56.40 53.57 54.56 0.58 0.63 0.56 1.63 1.70 1.73
ZNF300 ENST00000446148 56.41 45.18 49.72 0.58 0.70 0.66 1.63 1.98 1.85
UPK3A ENST00000216211 56.41 88.21 75.21 0.58 0.23 0.37 1.63 0.37 0.67
TMEM37 ENST00000306406 56.42 86.42 74.27 0.58 0.24 0.39 1.64 0.42 0.69
MRPL51 ENST00000229238 56.42 69.97 64.51 0.58 0.53 0.51 1.64 1.14 1.34
UGGT2 ENST00000376747 56.43 56.59 56.28 0.58 0.53 0.49 1.64 1.55 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.