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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
SLC37A4 ENST00000357590 26.61 47.99 35.48 1.32 0.62 0.87 1.32 2.00 1.78
CABIN1 ENST00000398319 26.61 29.80 26.32 1.32 1.13 1.00 1.32 1.40 1.25
SYT9 ENST00000318881 26.62 23.88 23.38 1.32 1.39 1.19 1.32 0.95 0.99
DGKB ENST00000403951 26.62 15.36 18.99 1.32 1.90 1.54 1.32 0.68 0.83
EHD2 ENST00000263277 26.63 27.79 25.29 1.32 1.23 1.05 1.32 1.18 1.16
AP3M2 ENST00000518421 26.63 60.39 41.73 1.30 0.53 0.72 1.33 1.41 2.01
KIAA0232 ENST00000307659 26.64 5.65 13.75 1.30 2.97 2.07 1.33 0.33 0.57
DLX3 ENST00000434704 26.64 52.95 38.07 1.30 0.63 0.86 1.32 1.78 2.02
PSMB2 ENST00000373237 26.65 17.54 20.16 1.30 1.58 1.48 1.32 0.73 0.88
URGCP ENST00000453200 26.65 18.75 20.84 1.30 1.52 1.46 1.32 0.74 0.87
SOST ENST00000301691 26.66 21.54 22.25 1.30 1.43 1.16 1.32 0.81 0.96
CHRD ENST00000204604 26.66 26.16 24.45 1.30 1.19 1.08 1.32 1.08 1.08
FILIP1 ENST00000237172 26.67 36.53 29.76 1.30 0.78 0.86 1.32 1.63 1.42
NARS ENST00000256854 26.67 41.35 32.22 1.30 0.62 0.91 1.32 1.81 1.60
MED4 ENST00000258648 26.68 41.26 32.18 1.30 0.61 0.91 1.32 1.82 1.60
ZSWIM3 ENST00000255152 26.68 43.05 33.02 1.30 0.61 0.85 1.33 1.89 1.66
TMX2 ENST00000278422 26.69 23.62 23.22 1.29 1.39 1.19 1.33 0.93 1.01
USP31 ENST00000219689 26.69 18.54 20.75 1.29 1.49 1.46 1.34 0.76 0.89
PLEKHM2 ENST00000375799 26.70 27.02 24.89 1.30 1.23 1.02 1.34 1.12 1.11
DNAJC5B ENST00000276570 26.70 82.24 53.93 1.30 0.34 0.61 1.34 0.52 1.77
GMEB2 ENST00000266068 26.71 7.99 15.12 1.30 2.56 1.86 1.34 0.44 0.64
AHR ENST00000242057 26.71 3.38 12.61 1.30 3.43 2.20 1.34 0.29 0.52
COPG1 ENST00000314797 26.72 19.25 21.12 1.30 1.47 1.42 1.34 0.75 0.90
ANKRA2 ENST00000296785 26.72 63.46 43.47 1.30 0.49 0.62 1.34 1.26 2.00
SEPT1 ENST00000605106 26.73 61.34 42.30 1.30 0.54 0.70 1.34 1.40 2.01

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