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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
ACSL5 ENST00000356116 41.33 37.85 37.82 0.84 0.80 0.84 1.68 1.70 2.02
ITM2C ENST00000326427 41.33 24.83 31.32 0.84 1.33 0.87 1.68 1.06 1.55
TMEM63C ENST00000298351 41.34 16.80 27.20 0.84 1.67 0.99 1.68 0.71 1.25
NME9 ENST00000383180 41.34 63.66 51.66 0.84 0.49 0.62 1.68 1.23 1.93
ZCCHC9 ENST00000254037 41.35 50.16 44.23 0.84 0.67 0.62 1.68 1.99 2.04
DNAJC17 ENST00000220496 41.35 38.28 38.08 0.84 0.75 0.86 1.68 1.71 2.02
SNX4 ENST00000251775 41.36 43.76 40.74 0.84 0.62 0.81 1.68 1.95 2.05
ADAMTS15 ENST00000299164 41.36 37.81 37.81 0.84 0.80 0.84 1.68 1.69 2.02
OGFOD1 ENST00000566157 41.37 67.18 53.69 0.84 0.54 0.62 1.68 1.22 1.80
ORAI3 ENST00000318663 41.37 68.66 54.58 0.84 0.53 0.56 1.68 1.18 1.73
SH3GL3 ENST00000427482 41.38 40.65 39.37 0.84 0.63 0.80 1.68 1.77 2.04
BACH1 ENST00000399921 41.38 21.30 29.53 0.84 1.42 0.84 1.68 0.81 1.37
CBX7 ENST00000216133 41.39 25.66 31.72 0.84 1.24 0.89 1.68 1.05 1.58
SLC26A2 ENST00000286298 41.39 61.97 50.76 0.84 0.56 0.66 1.68 1.37 1.84
DOCK8 ENST00000453981 41.40 22.81 30.29 0.82 1.46 0.84 1.68 0.88 1.44
GABPB2 ENST00000368918 41.40 43.92 40.83 0.82 0.61 0.80 1.68 1.97 2.04
CTSH ENST00000220166 41.41 50.02 44.15 0.82 0.66 0.61 1.68 2.01 2.04
PLEKHB2 ENST00000409158 41.41 76.95 59.45 0.82 0.43 0.49 1.68 0.79 1.70
NMD3 ENST00000460469 41.42 45.95 41.91 0.82 0.76 0.68 1.68 2.02 2.01
TOP3B ENST00000398793 41.42 28.03 32.89 0.82 1.20 0.86 1.69 1.19 1.67
HDHD2 ENST00000300605 41.43 78.91 60.75 0.82 0.40 0.44 1.69 0.70 1.61
COQ10B ENST00000263960 41.43 33.38 35.55 0.82 0.85 0.85 1.68 1.50 1.78
MAL2 ENST00000276681 41.44 62.89 51.24 0.82 0.51 0.63 1.68 1.30 1.92
CNRIP1 ENST00000263655 41.44 58.81 48.99 0.82 0.54 0.72 1.68 1.41 1.84
HTR1D ENST00000374619 41.45 71.27 56.09 0.82 0.53 0.49 1.68 1.07 1.77

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