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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
ELK3 ENST00000228741 16.79 36.86 24.86 1.46 0.76 1.02 0.84 1.67 1.10
TUBGCP4 ENST00000564079 16.80 37.19 25.05 1.46 0.78 1.05 0.85 1.66 1.15
CREB5 ENST00000357727 16.80 23.04 17.81 1.47 1.44 1.66 0.85 0.91 0.78
ARHGAP32 ENST00000310343 16.81 9.25 10.63 1.47 2.47 2.16 0.85 0.47 0.43
FAM19A2 ENST00000416284 16.81 37.85 25.41 1.47 0.80 1.04 0.86 1.70 1.17
MARK4 ENST00000262891 16.82 7.24 9.46 1.47 2.58 2.30 0.86 0.37 0.40
SLC9A2 ENST00000233969 16.82 26.99 19.95 1.47 1.23 1.46 0.86 1.12 0.84
C9orf78 ENST00000372447 16.83 53.43 33.30 1.47 0.65 0.89 0.86 1.70 1.70
TMEM170B ENST00000379426 16.83 29.34 21.20 1.48 1.11 1.40 0.86 1.36 0.90
TRIM44 ENST00000299413 16.84 33.29 23.16 1.48 0.84 1.19 0.86 1.50 1.01
NXT2 ENST00000218004 16.84 26.24 19.56 1.47 1.19 1.53 0.86 1.08 0.84
SLC6A8 ENST00000253122 16.85 7.41 9.58 1.47 2.53 2.28 0.86 0.39 0.40
OTUD6B ENST00000285420 16.85 69.58 41.45 1.47 0.52 0.73 0.86 1.10 2.02
SBK1 ENST00000341901 16.86 38.74 25.95 1.47 0.70 0.99 0.86 1.67 1.25
ST3GAL4 ENST00000526727 16.86 32.27 22.74 1.47 0.86 1.18 0.86 1.45 0.98
OPCML ENST00000331898 16.87 29.02 21.08 1.48 1.15 1.42 0.86 1.31 0.89
PCNX ENST00000304743 16.87 6.79 9.29 1.48 2.66 2.32 0.86 0.37 0.38
PAX8 ENST00000429538 16.88 6.16 8.90 1.48 2.75 2.49 0.86 0.35 0.38
UCHL3 ENST00000377595 16.88 64.24 38.89 1.47 0.49 0.80 0.86 1.20 2.05
NADK ENST00000344463 16.89 54.65 33.93 1.47 0.58 0.90 0.86 1.65 1.73
RRM2B ENST00000251810 16.89 36.02 24.52 1.48 0.80 1.08 0.86 1.58 1.08
PRODH ENST00000357068 16.90 59.43 36.28 1.48 0.52 0.85 0.86 1.41 1.85
GTF2F2 ENST00000340473 16.91 45.29 29.25 1.48 0.70 0.84 0.86 1.97 1.34
EYA4 ENST00000367895 16.91 21.39 17.01 1.48 1.44 1.67 0.86 0.80 0.70
SLC35F3 ENST00000366618 16.92 25.15 19.03 1.48 1.32 1.54 0.86 1.03 0.85

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