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
SURF2 ENST00000371964 94.38 74.97 87.79 0.10 0.53 0.24 0.11 0.93 0.32
SLC22A11 ENST00000301891 94.38 55.51 78.20 0.10 0.56 0.39 0.11 1.60 0.55
ZNF730 ENST00000597761 94.39 90.40 95.13 0.10 0.25 0.09 0.11 0.37 0.10
MBD3L2 ENST00000381393 94.39 98.91 98.80 0.10 0.17 0.10 0.11 0.14 0.05
GOLGA8O ENST00000509311 94.40 93.62 96.82 0.10 0.28 0.08 0.11 0.28 0.07
CCDC144NL ENST00000327925 94.40 96.72 98.02 0.10 0.23 0.09 0.11 0.19 0.05
NUTM2D ENST00000412718 94.41 58.46 79.74 0.10 0.54 0.38 0.11 1.39 0.53
C10orf95 ENST00000239125 94.41 94.15 97.04 0.10 0.25 0.08 0.11 0.25 0.07
DAND5 ENST00000317060 94.42 90.34 95.11 0.10 0.25 0.09 0.11 0.38 0.10
ZNF681 ENST00000402377 94.42 82.36 91.29 0.10 0.34 0.15 0.11 0.52 0.18
GOLGA8R ENST00000327271 94.43 97.43 98.25 0.10 0.22 0.09 0.11 0.19 0.05
AC003101.1 ENST00000412403 94.43 92.54 96.22 0.10 0.29 0.07 0.11 0.31 0.09
AKAP14 ENST00000371431 94.44 36.40 67.19 0.10 0.82 0.52 0.11 1.63 1.16
CORT ENST00000377049 94.44 96.27 97.88 0.10 0.22 0.09 0.11 0.19 0.04
CGB5 ENST00000301408 94.45 92.96 96.47 0.10 0.29 0.07 0.11 0.30 0.08
TRIM48 ENST00000417545 94.45 97.49 98.30 0.10 0.22 0.09 0.11 0.19 0.05
GOLGA8K ENST00000512626 94.46 95.42 97.56 0.10 0.24 0.08 0.11 0.20 0.06
C3orf83 ENST00000564146 94.46 85.67 92.82 0.10 0.27 0.14 0.11 0.44 0.15
ADGB ENST00000397944 94.47 42.82 71.06 0.10 0.63 0.43 0.11 1.92 0.86
ANKRD20A4 ENST00000357336 94.47 95.85 97.75 0.10 0.22 0.09 0.11 0.20 0.05
C2orf72 ENST00000373640 94.48 86.17 93.06 0.10 0.27 0.14 0.11 0.42 0.15
SIGLEC5 ENST00000570106 94.48 56.15 78.58 0.10 0.52 0.38 0.11 1.55 0.55
SIGLEC5 ENST00000429354 94.49 56.41 78.70 0.10 0.52 0.38 0.11 1.53 0.54
CLLU1 ENST00000378485 94.49 90.39 95.20 0.10 0.25 0.08 0.11 0.37 0.10
C1orf167 ENST00000433342 94.50 60.29 80.72 0.10 0.53 0.39 0.11 1.39 0.52

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.