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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
CTPS1 ENST00000372621 4.40 11.33 5.12 3.72 2.11 3.62 0.30 0.56 0.25
BTK ENST00000308731 4.40 1.15 1.03 3.72 3.99 4.45 0.30 0.28 0.21
EXOC7 ENST00000335146 4.41 34.55 17.35 3.71 0.80 1.63 0.30 1.54 0.75
TUBG1 ENST00000251413 4.41 27.43 13.55 3.71 1.25 2.05 0.29 1.17 0.57
SCN3A ENST00000283254 4.42 3.33 1.76 3.71 3.42 4.22 0.29 0.27 0.23
LRRC8D ENST00000337338 4.42 13.45 6.18 3.71 2.05 3.19 0.29 0.60 0.31
TRIM33 ENST00000358465 4.43 0.72 0.91 3.71 4.10 4.48 0.29 0.28 0.21
LSM12 ENST00000591247 4.43 10.25 4.68 3.70 2.28 3.69 0.29 0.49 0.25
EIF4G1 ENST00000424196 4.44 0.45 0.83 3.70 4.11 4.54 0.29 0.28 0.21
TNIK ENST00000436636 4.44 4.67 2.23 3.70 3.27 4.06 0.29 0.31 0.23
EIF2S2 ENST00000374980 4.45 15.01 7.09 3.70 1.91 2.86 0.29 0.64 0.33
MED23 ENST00000368068 4.45 24.25 11.97 3.70 1.30 2.28 0.29 0.99 0.47
DNMT1 ENST00000359526 4.46 1.61 1.19 3.71 3.87 4.44 0.29 0.26 0.21
CBX3 ENST00000337620 4.46 13.74 6.42 3.71 2.05 3.06 0.29 0.59 0.32
FOXP2 ENST00000408937 4.47 5.05 2.43 3.70 3.21 4.02 0.29 0.32 0.23
MFAP1 ENST00000267812 4.47 16.63 7.93 3.70 1.72 2.61 0.29 0.71 0.36
KLHL24 ENST00000454652 4.48 33.62 16.88 3.70 0.85 1.68 0.29 1.55 0.70
CDK5 ENST00000485972 4.48 30.96 15.55 3.70 1.05 1.78 0.29 1.36 0.67
TRAF3 ENST00000560371 4.49 6.85 3.11 3.70 2.62 3.93 0.29 0.37 0.24
ZMYM4 ENST00000314607 4.49 0.98 1.01 3.71 4.09 4.46 0.29 0.29 0.21
INTS6 ENST00000311234 4.50 2.51 1.50 3.70 3.56 4.34 0.29 0.29 0.22
ADIPOR2 ENST00000357103 4.50 26.11 12.85 3.70 1.20 2.11 0.29 1.09 0.53
FADS2 ENST00000278840 4.51 8.83 4.00 3.70 2.47 3.76 0.29 0.48 0.23
ACTG2 ENST00000409624 4.51 32.60 16.36 3.70 0.86 1.71 0.29 1.47 0.67
CNOT8 ENST00000517876 4.52 32.30 16.21 3.70 0.86 1.71 0.29 1.46 0.65

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