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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
VTA1 ENST00000367630 28.80 48.60 36.91 1.11 0.63 0.81 1.54 2.01 1.94
E2F8 ENST00000527884 28.81 17.08 21.07 1.11 1.62 1.42 1.54 0.74 0.89
SLC5A1 ENST00000266088 28.81 39.52 32.36 1.11 0.68 0.91 1.53 1.63 1.61
SLCO5A1 ENST00000260126 28.82 38.31 31.79 1.11 0.75 0.89 1.54 1.71 1.58
NOTCH3 ENST00000263388 28.82 12.76 18.80 1.11 2.09 1.57 1.54 0.59 0.82
POLDIP2 ENST00000540200 28.83 22.93 23.95 1.11 1.47 1.09 1.54 0.90 1.05
PHKG2 ENST00000563588 28.83 33.80 29.48 1.11 0.85 0.85 1.54 1.55 1.38
ISL2 ENST00000290759 28.84 35.19 30.19 1.11 0.76 0.81 1.55 1.58 1.45
ID4 ENST00000378700 28.84 90.79 60.28 1.11 0.25 0.47 1.55 0.35 1.60
ACBD3 ENST00000366812 28.85 27.20 26.20 1.11 1.25 0.99 1.55 1.15 1.25
TAF6L ENST00000294168 28.85 23.40 24.14 1.11 1.42 1.11 1.55 0.93 1.06
HS2ST1 ENST00000370550 28.86 23.80 24.40 1.11 1.38 1.08 1.54 0.93 1.08
SORBS1 ENST00000371247 28.86 30.70 27.94 1.10 1.05 0.85 1.54 1.37 1.28
ENPP1 ENST00000360971 28.87 30.89 28.07 1.10 1.08 0.81 1.53 1.36 1.28
KIAA2018 ENST00000316407 28.87 4.94 14.65 1.10 3.26 1.96 1.53 0.32 0.59
CLTB ENST00000310418 28.88 30.01 27.56 1.10 1.09 0.96 1.53 1.43 1.27
DEK ENST00000397239 28.88 29.37 27.24 1.10 1.10 0.99 1.53 1.36 1.25
LTN1 ENST00000389194 28.89 16.25 20.67 1.10 1.80 1.47 1.53 0.69 0.88
CHMP5 ENST00000223500 28.89 43.20 34.32 1.10 0.62 0.87 1.53 1.92 1.76
SERF2 ENST00000409960 28.90 76.67 51.98 1.10 0.40 0.62 1.53 0.83 1.92
TMEM246 ENST00000374851 28.90 40.58 32.91 1.10 0.63 0.86 1.53 1.77 1.67
RYR3 ENST00000389232 28.91 10.89 17.79 1.10 2.11 1.66 1.53 0.50 0.78
TMEM256 ENST00000302422 28.91 89.56 59.54 1.10 0.27 0.49 1.53 0.37 1.69
TUBB6 ENST00000317702 28.92 56.99 41.15 1.10 0.56 0.75 1.53 1.53 2.02
CDH18 ENST00000507958 28.92 22.16 23.64 1.10 1.52 1.19 1.54 0.82 1.01

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