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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
SLC44A5 ENST00000370855 20.02 27.40 21.85 1.53 1.25 1.21 1.00 1.17 0.95
SLITRK1 ENST00000377084 20.02 14.08 14.82 1.53 2.07 1.96 1.00 0.59 0.62
FAM13B ENST00000033079 20.03 15.12 15.34 1.53 1.91 1.80 1.00 0.66 0.66
MYO9A ENST00000356056 20.04 11.87 13.58 1.53 2.10 2.02 1.00 0.58 0.57
MED6 ENST00000256379 20.04 53.74 35.04 1.53 0.63 0.87 1.00 1.70 1.75
RBP7 ENST00000294435 20.05 40.52 28.47 1.53 0.63 0.78 1.00 1.77 1.29
MMS19 ENST00000438925 20.05 16.06 15.86 1.53 1.82 1.77 1.00 0.68 0.66
KLHL8 ENST00000273963 20.06 38.89 27.62 1.54 0.70 0.96 1.00 1.65 1.26
CDC42SE1 ENST00000439374 20.06 85.40 51.90 1.54 0.25 0.62 1.01 0.45 1.94
CYR61 ENST00000451137 20.07 24.40 20.30 1.54 1.29 1.47 1.01 1.00 0.89
BIRC3 ENST00000263464 20.07 26.76 21.55 1.54 1.21 1.28 1.01 1.12 0.93
MB21D2 ENST00000392452 20.08 37.33 26.88 1.54 0.76 0.97 1.01 1.65 1.27
ACTN2 ENST00000366578 20.08 8.13 11.73 1.53 2.53 2.21 1.01 0.44 0.47
COL5A2 ENST00000374866 20.09 1.03 7.93 1.53 4.05 2.61 1.00 0.28 0.36
MAP3K13 ENST00000265026 20.09 15.36 15.54 1.53 1.90 1.80 1.00 0.68 0.67
ZNF689 ENST00000287461 20.10 24.48 20.34 1.53 1.32 1.48 1.00 1.01 0.88
RNF214 ENST00000531452 20.10 15.15 15.43 1.53 1.90 1.82 1.00 0.66 0.67
LSM1 ENST00000311351 20.11 68.26 42.45 1.53 0.52 0.68 1.00 1.21 2.01
CCDC47 ENST00000225726 20.11 48.25 32.40 1.53 0.63 0.91 1.00 1.99 1.61
SLC6A9 ENST00000360584 20.12 34.10 25.18 1.53 0.84 1.05 1.00 1.53 1.16
MKX ENST00000375790 20.12 19.97 17.97 1.53 1.46 1.70 1.00 0.73 0.78
EPHX4 ENST00000370383 20.13 51.13 33.80 1.53 0.66 0.89 1.00 1.91 1.74
CDK4 ENST00000257904 20.13 32.04 24.10 1.53 0.92 1.09 1.00 1.47 1.06
SHPRH ENST00000367505 20.14 19.77 17.88 1.53 1.42 1.68 1.00 0.74 0.77
CA8 ENST00000317995 20.14 30.89 23.62 1.53 1.08 1.19 1.00 1.36 1.01

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