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
PNPLA5 ENST00000216177 74.51 58.65 68.56 0.37 0.54 0.47 0.79 1.42 1.05
MTNR1A ENST00000307161 74.52 88.87 85.06 0.37 0.25 0.33 0.79 0.35 0.38
CLCA4 ENST00000370563 74.52 59.72 69.23 0.37 0.52 0.44 0.79 1.39 0.98
EFHB ENST00000295824 74.53 70.68 75.57 0.38 0.49 0.38 0.79 1.09 0.64
BEX4 ENST00000372695 74.53 42.65 58.67 0.38 0.59 0.52 0.79 1.90 1.65
UNC93B1 ENST00000227471 74.54 23.00 47.52 0.38 1.44 0.63 0.79 0.91 1.89
MVD ENST00000301012 74.54 86.17 83.74 0.38 0.27 0.34 0.79 0.42 0.41
PLA2G2D ENST00000375105 74.55 89.02 85.14 0.38 0.27 0.33 0.79 0.35 0.37
SULT1A2 ENST00000395630 74.55 83.34 82.30 0.38 0.27 0.33 0.79 0.47 0.45
PTPN18 ENST00000175756 74.56 51.66 64.38 0.38 0.62 0.51 0.79 1.87 1.34
CALCA ENST00000331587 74.56 85.00 83.17 0.38 0.25 0.29 0.79 0.45 0.40
CCDC14 ENST00000433542 74.57 51.75 64.45 0.38 0.61 0.51 0.79 1.89 1.34
FAM217A ENST00000274673 74.57 60.68 69.85 0.38 0.54 0.46 0.79 1.40 0.92
MFI2 ENST00000296350 74.58 59.66 69.22 0.38 0.52 0.44 0.79 1.40 0.98
C9orf156 ENST00000375119 74.58 68.57 74.48 0.38 0.53 0.40 0.79 1.19 0.69
FAN1 ENST00000362065 74.59 61.43 70.30 0.38 0.54 0.43 0.79 1.39 0.91
GLRX ENST00000379979 74.59 95.83 88.37 0.38 0.22 0.22 0.79 0.20 0.30
NRIP2 ENST00000337508 74.60 80.47 80.85 0.38 0.37 0.39 0.79 0.59 0.51
FGF21 ENST00000593756 74.60 71.30 75.97 0.38 0.53 0.38 0.79 1.07 0.62
RAMP3 ENST00000242249 74.61 84.01 82.72 0.38 0.27 0.32 0.79 0.45 0.42
RHBDL1 ENST00000219551 74.61 27.55 50.09 0.38 1.25 0.62 0.79 1.17 1.92
ALOX15 ENST00000570836 74.62 75.29 78.21 0.38 0.49 0.39 0.79 0.90 0.55
CLN8 ENST00000331222 74.62 67.24 73.74 0.38 0.56 0.42 0.79 1.22 0.71
MKI67IP ENST00000285814 74.63 53.47 65.64 0.38 0.65 0.51 0.79 1.72 1.29
CXorf38 ENST00000327877 74.63 66.60 73.39 0.38 0.54 0.42 0.79 1.22 0.77

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.