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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
EPB41L3 ENST00000341928 24.28 23.34 21.93 1.35 1.42 1.18 1.12 0.93 0.97
SIM1 ENST00000369208 24.29 9.40 14.58 1.35 2.48 1.97 1.12 0.49 0.59
DCAF6 ENST00000367840 24.29 16.23 18.22 1.35 1.80 1.64 1.12 0.69 0.79
TTC13 ENST00000366661 24.30 23.92 22.25 1.35 1.39 1.16 1.12 0.95 0.96
ATCAY ENST00000450849 24.30 21.12 20.88 1.35 1.47 1.46 1.12 0.82 0.87
APOA1 ENST00000236850 24.31 73.58 47.78 1.35 0.52 0.65 1.12 1.03 1.88
SETDB2 ENST00000317257 24.31 30.98 25.77 1.35 1.04 1.04 1.12 1.36 1.23
SKIL ENST00000458537 24.32 12.90 16.41 1.35 2.07 1.71 1.12 0.59 0.68
ORAI2 ENST00000356387 24.32 47.61 34.18 1.35 0.62 0.89 1.12 1.99 1.75
A1CF ENST00000373995 24.33 47.59 34.17 1.34 0.61 0.89 1.12 2.00 1.75
RBM12 ENST00000374114 24.33 42.44 31.60 1.34 0.59 0.89 1.12 1.89 1.57
ECE1 ENST00000374893 24.34 13.95 16.99 1.34 2.05 1.67 1.12 0.60 0.70
SLC35A1 ENST00000369552 24.34 22.23 21.42 1.34 1.53 1.33 1.12 0.81 0.91
NR1D1 ENST00000246672 24.35 18.93 19.63 1.34 1.52 1.53 1.12 0.76 0.85
PDK2 ENST00000503176 24.35 50.16 35.46 1.34 0.67 0.87 1.12 1.99 1.77
ALDH6A1 ENST00000553458 24.36 52.93 36.85 1.34 0.63 0.81 1.12 1.78 1.94
ICK ENST00000356971 24.36 33.59 27.14 1.34 0.85 0.99 1.12 1.55 1.26
PTCH1 ENST00000331920 24.37 0.43 9.95 1.34 4.13 2.28 1.12 0.28 0.42
GAD2 ENST00000376261 24.37 17.44 18.90 1.34 1.59 1.54 1.12 0.74 0.83
AEBP2 ENST00000398864 24.38 2.90 11.30 1.34 3.49 2.16 1.12 0.29 0.45
MRPL33 ENST00000296102 24.38 55.00 37.96 1.33 0.57 0.85 1.12 1.64 2.02
G6PC3 ENST00000269097 24.39 56.97 39.02 1.33 0.56 0.78 1.12 1.53 2.07
HECW1 ENST00000395891 24.39 8.38 14.09 1.33 2.52 2.04 1.12 0.46 0.60
F2 ENST00000311907 24.40 27.41 23.93 1.33 1.25 1.09 1.12 1.17 1.04
IL1RAP ENST00000317757 24.40 21.30 20.98 1.33 1.42 1.43 1.12 0.81 0.88

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