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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
NECAB1 ENST00000417640 45.07 31.02 36.17 0.65 1.05 0.87 1.74 1.36 1.81
ANKRD29 ENST00000592179 45.08 68.77 56.73 0.65 0.53 0.52 1.74 1.18 1.70
HCRTR1 ENST00000403528 45.08 46.94 44.55 0.65 0.71 0.62 1.74 1.94 2.04
TSR1 ENST00000301364 45.09 61.57 52.65 0.63 0.54 0.59 1.75 1.41 1.89
THAP9 ENST00000302236 45.09 52.28 47.45 0.63 0.62 0.63 1.75 1.84 1.87
PUS1 ENST00000376649 45.10 46.99 44.59 0.63 0.70 0.62 1.75 1.97 2.05
KARS ENST00000319410 45.10 49.21 45.85 0.63 0.66 0.68 1.75 2.03 1.97
ODF1 ENST00000285402 45.11 10.01 25.64 0.63 2.35 1.06 1.75 0.49 1.21
ZSCAN18 ENST00000600404 45.11 35.66 38.65 0.63 0.78 0.82 1.75 1.57 2.01
POLA2 ENST00000265465 45.12 32.04 36.77 0.63 0.92 0.82 1.74 1.47 1.94
LIPH ENST00000296252 45.12 66.25 55.33 0.63 0.53 0.49 1.73 1.20 1.73
ZFYVE16 ENST00000338008 45.13 37.43 39.65 0.63 0.76 0.80 1.74 1.66 2.05
KCNAB3 ENST00000303790 45.13 64.70 54.48 0.63 0.48 0.57 1.74 1.24 1.76
RFC3 ENST00000380071 45.14 51.75 47.20 0.63 0.61 0.67 1.74 1.89 1.89
GNL3 ENST00000418458 45.14 72.59 59.01 0.63 0.47 0.48 1.74 1.04 1.65
PLAC8 ENST00000426923 45.15 63.68 53.87 0.63 0.49 0.61 1.75 1.23 1.78
OARD1 ENST00000479950 45.15 72.30 58.82 0.63 0.51 0.51 1.75 1.03 1.65
OTUD3 ENST00000375120 45.16 53.28 48.08 0.63 0.66 0.66 1.75 1.72 1.88
PNPLA8 ENST00000422087 45.16 25.98 33.73 0.63 1.20 0.89 1.75 1.10 1.73
TMEM88 ENST00000301599 45.17 66.17 55.30 0.63 0.53 0.51 1.75 1.20 1.73
C20orf24 ENST00000342422 45.17 31.62 36.50 0.65 0.95 0.85 1.75 1.44 1.89
LIG4 ENST00000356922 45.18 41.30 41.46 0.65 0.62 0.73 1.75 1.82 2.02
OIT3 ENST00000334011 45.18 64.02 54.10 0.65 0.49 0.59 1.75 1.20 1.76
CDH4 ENST00000360469 45.19 15.84 28.67 0.65 1.89 0.80 1.75 0.68 1.34
ZCWPW1 ENST00000398027 45.19 53.90 48.41 0.63 0.65 0.67 1.75 1.70 1.87

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