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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
CSF3R ENST00000373103 40.11 41.42 39.12 0.86 0.62 0.77 1.75 1.80 2.06
MOGS ENST00000233616 40.52 51.79 44.74 0.86 0.61 0.63 1.75 1.89 2.06
DTNB ENST00000406818 40.91 40.40 38.99 0.84 0.61 0.80 1.72 1.76 2.06
ZMYND15 ENST00000573751 41.02 51.25 44.71 0.85 0.65 0.62 1.71 1.90 2.06
TBC1D8B ENST00000357242 41.57 39.83 39.03 0.81 0.65 0.78 1.71 1.68 2.06
CBS ENST00000398165 42.38 38.96 39.01 0.76 0.70 0.80 1.75 1.64 2.06
KIF27 ENST00000297814 42.96 49.30 44.72 0.81 0.65 0.63 1.77 2.02 2.06
RELL2 ENST00000297164 42.97 38.29 38.97 0.81 0.75 0.80 1.77 1.72 2.06
ATP1B4 ENST00000218008 43.60 48.68 44.72 0.76 0.63 0.63 1.80 1.99 2.06
CFB ENST00000456570 44.01 37.24 38.95 0.73 0.76 0.80 1.77 1.66 2.06
ELOVL7 ENST00000508821 44.53 36.96 39.09 0.65 0.75 0.77 1.80 1.70 2.06
ADAMTS5 ENST00000284987 44.54 36.72 38.96 0.65 0.76 0.80 1.80 1.66 2.06
MLST8 ENST00000569417 46.05 35.26 38.99 0.58 0.76 0.80 1.80 1.58 2.06
PAK6 ENST00000560346 47.36 38.11 40.94 0.56 0.77 0.78 1.82 1.70 2.06
ZNF653 ENST00000293771 48.31 33.03 39.01 0.56 0.85 0.78 1.81 1.49 2.06
NDN ENST00000331837 48.66 32.94 39.17 0.51 0.82 0.78 1.83 1.46 2.06
EFNA3 ENST00000505139 49.59 31.64 38.94 0.54 0.95 0.80 1.82 1.44 2.06
TUB ENST00000305253 51.78 29.48 38.96 0.58 1.10 0.80 1.82 1.39 2.06
PRRT2 ENST00000567659 52.06 29.31 39.02 0.59 1.14 0.78 1.84 1.36 2.06
SEMA4B ENST00000411539 52.80 28.70 39.10 0.66 1.16 0.77 1.77 1.29 2.06
C15orf39 ENST00000360639 53.57 28.00 39.15 0.62 1.20 0.77 1.75 1.18 2.06
LOXL2 ENST00000389131 53.62 31.78 40.90 0.62 0.94 0.78 1.77 1.48 2.06
ZNF804A ENST00000302277 59.93 21.40 39.00 0.63 1.43 0.80 1.39 0.80 2.06
SMOC2 ENST00000354536 60.40 31.74 44.64 0.59 0.95 0.62 1.38 1.48 2.06
GFRA2 ENST00000524240 60.57 31.72 44.73 0.58 0.95 0.63 1.35 1.47 2.06

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