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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
TRIM49C ENST00000448984 97.77 77.79 90.85 0.11 0.42 0.15 0.10 0.79 0.20
IBA57-AS1 ENST00000366713 98.38 98.65 99.74 0.10 0.20 0.12 0.10 0.15 0.04
SIGLEC8 ENST00000321424 97.78 60.37 82.48 0.11 0.53 0.33 0.10 1.41 0.43
BTN3A3 ENST00000244519 98.38 84.35 94.12 0.10 0.29 0.09 0.10 0.44 0.12
LUZP4 ENST00000371920 97.78 92.00 97.49 0.11 0.23 0.08 0.10 0.33 0.07
FSCB ENST00000340446 98.39 97.59 99.50 0.10 0.22 0.11 0.10 0.20 0.05
S100A9 ENST00000368738 97.79 80.35 91.83 0.11 0.37 0.14 0.10 0.59 0.17
RP11-321M21.3 ENST00000578340 97.19 95.98 98.67 0.10 0.22 0.10 0.10 0.20 0.05
BTN3A1 ENST00000289361 98.39 65.76 85.44 0.10 0.54 0.34 0.10 1.22 0.35
C4orf6 ENST00000195455 97.79 97.44 99.29 0.11 0.22 0.11 0.11 0.19 0.04
SPESP1 ENST00000310673 97.20 86.66 94.65 0.10 0.24 0.09 0.11 0.40 0.11
GALP ENST00000357330 98.40 86.12 95.00 0.10 0.27 0.09 0.11 0.43 0.10
CEMP1 ENST00000382350 97.80 98.21 99.54 0.11 0.20 0.12 0.11 0.15 0.05
HAVCR1 ENST00000339252 97.20 73.22 88.36 0.10 0.54 0.22 0.11 1.02 0.30
WFDC8 ENST00000357199 98.40 76.13 90.31 0.10 0.43 0.15 0.11 0.87 0.21
MYEOV ENST00000308946 97.80 95.86 98.86 0.11 0.22 0.10 0.11 0.20 0.05
PSAPL1 ENST00000319098 97.21 99.28 99.61 0.10 0.15 0.12 0.11 0.12 0.05
RFPL4AL1 ENST00000341750 98.41 81.07 92.45 0.10 0.35 0.14 0.11 0.55 0.15
TMIGD2 ENST00000301272 97.81 81.78 92.53 0.11 0.34 0.14 0.11 0.51 0.15
AC110781.3 ENST00000402221 97.21 92.30 97.38 0.10 0.25 0.08 0.11 0.30 0.07
ANKRD60 ENST00000457363 96.01 88.28 94.90 0.11 0.23 0.09 0.11 0.37 0.11
IL37 ENST00000263326 96.02 87.57 94.54 0.11 0.23 0.10 0.11 0.37 0.12
CLPSL1 ENST00000373861 97.22 95.64 98.60 0.10 0.23 0.10 0.11 0.21 0.05
ZNF439 ENST00000304030 97.82 84.79 94.07 0.11 0.27 0.09 0.11 0.42 0.12
ZNF28 ENST00000457749 98.41 90.54 97.19 0.10 0.25 0.08 0.11 0.37 0.06

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