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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
JKAMP ENST00000261247 17.82 33.91 23.89 1.52 0.84 1.09 0.90 1.55 1.04
SSH1 ENST00000326495 17.83 26.58 20.26 1.52 1.19 1.48 0.90 1.12 0.88
NANOG ENST00000229307 17.83 29.14 21.62 1.52 1.14 1.27 0.90 1.34 0.93
NBEA ENST00000400445 17.84 0.15 6.32 1.52 4.13 3.11 0.90 0.28 0.32
PIK3C2A ENST00000265970 17.85 16.80 15.11 1.52 1.67 1.86 0.90 0.71 0.63
SNX2 ENST00000379516 17.85 13.09 13.05 1.52 2.06 2.09 0.90 0.59 0.52
LTB ENST00000429299 17.86 94.13 55.68 1.52 0.25 0.53 0.90 0.25 1.73
SP5 ENST00000375281 17.86 30.25 22.19 1.52 1.09 1.15 0.90 1.40 0.96
FGF8 ENST00000320185 17.87 26.80 20.42 1.53 1.23 1.51 0.90 1.12 0.88
PTPRM ENST00000580170 17.87 7.00 9.98 1.53 2.57 2.25 0.90 0.37 0.42
EXT1 ENST00000378204 17.88 9.58 11.39 1.53 2.49 2.19 0.90 0.50 0.45
MGA ENST00000219905 17.88 0.54 6.58 1.53 4.16 3.00 0.90 0.27 0.32
SMIM14 ENST00000295958 17.89 30.30 22.23 1.53 1.08 1.15 0.90 1.40 0.96
FAM32A ENST00000263384 17.89 61.77 38.09 1.53 0.57 0.86 0.90 1.37 2.02
FAM78B ENST00000338353 17.90 39.09 26.62 1.53 0.70 0.97 0.90 1.63 1.25
FAM131A ENST00000383847 17.90 38.26 26.25 1.53 0.75 1.01 0.90 1.70 1.26
ATG9A ENST00000409618 17.91 12.17 12.59 1.53 2.09 2.20 0.90 0.58 0.52
RNF208 ENST00000392827 17.91 25.32 19.65 1.53 1.28 1.53 0.90 1.03 0.85
PDE3A ENST00000359062 17.92 22.34 18.06 1.53 1.51 1.70 0.90 0.82 0.78
SLC33A1 ENST00000392845 17.92 43.72 28.98 1.53 0.62 0.81 0.90 1.95 1.31
MARK3 ENST00000429436 17.93 33.03 23.57 1.53 0.85 1.19 0.90 1.49 1.01
JTB ENST00000271843 17.93 32.96 23.54 1.53 0.84 1.19 0.90 1.47 1.01
EPHA6 ENST00000389672 17.94 15.95 14.69 1.53 1.89 1.96 0.90 0.68 0.61
TTYH1 ENST00000376531 17.94 9.14 11.19 1.53 2.48 2.16 0.90 0.47 0.45
SNRPN ENST00000400100 17.95 44.31 29.27 1.53 0.61 0.84 0.89 1.94 1.34

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