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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
SRR ENST00000344595 29.70 43.72 34.89 1.08 0.62 0.90 1.58 1.95 1.75
C17orf75 ENST00000577809 29.71 19.70 22.89 1.08 1.43 1.19 1.58 0.74 0.97
ST3GAL1 ENST00000319914 29.71 25.08 25.48 1.08 1.33 1.02 1.58 1.03 1.18
SUCO ENST00000263688 29.72 12.65 19.16 1.08 2.10 1.53 1.58 0.58 0.85
ISCU ENST00000311893 29.72 62.40 44.62 1.08 0.53 0.62 1.58 1.32 2.06
AXIN1 ENST00000262320 29.73 17.26 21.63 1.08 1.61 1.27 1.58 0.75 0.92
FBXW4 ENST00000331272 29.74 40.89 33.45 1.06 0.61 0.89 1.58 1.78 1.71
MYOT ENST00000239926 29.74 52.29 39.38 1.06 0.62 0.80 1.58 1.84 2.04
HOMER3 ENST00000539827 29.75 14.94 20.44 1.06 1.92 1.51 1.58 0.63 0.88
SLC30A2 ENST00000374276 29.75 33.82 29.97 1.06 0.85 0.85 1.58 1.56 1.46
SMYD2 ENST00000366957 29.76 46.33 36.14 1.06 0.73 0.87 1.58 2.04 1.80
CXorf21 ENST00000378962 29.76 23.84 24.83 1.06 1.38 1.02 1.58 0.93 1.11
CAPN7 ENST00000253693 29.77 42.14 34.15 1.05 0.61 0.89 1.58 1.87 1.75
LEPROT ENST00000371065 29.77 46.84 36.40 1.05 0.71 0.84 1.58 1.97 1.87
ST20-MTHFS ENST00000479961 29.78 71.98 49.84 1.05 0.51 0.65 1.58 1.05 1.89
YEATS2 ENST00000305135 29.78 9.88 17.73 1.05 2.35 1.66 1.59 0.50 0.78
ETV3 ENST00000368192 29.79 12.58 19.15 1.05 2.10 1.53 1.59 0.58 0.85
ADCY7 ENST00000394697 29.79 28.62 27.34 1.05 1.18 0.97 1.59 1.29 1.24
NUP43 ENST00000340413 29.80 45.72 35.85 1.05 0.75 0.86 1.59 2.02 1.78
GPD1L ENST00000282541 29.80 35.93 31.08 1.05 0.80 0.84 1.58 1.58 1.52
ZBTB4 ENST00000311403 29.81 1.83 13.43 1.05 3.78 2.05 1.59 0.26 0.56
ZZEF1 ENST00000381638 29.81 11.22 18.45 1.05 2.10 1.62 1.59 0.54 0.81
PAM ENST00000304400 29.82 25.45 25.73 1.05 1.25 1.04 1.59 1.05 1.22
ARPC5L ENST00000353214 29.82 39.59 32.88 1.05 0.68 0.86 1.59 1.66 1.67
MED18 ENST00000373842 29.83 89.00 59.76 1.05 0.27 0.49 1.59 0.35 1.66

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