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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
SELP ENST00000263686 75.29 72.57 77.08 0.37 0.47 0.37 0.76 1.04 0.61
OVCH2 ENST00000454689 75.29 94.85 88.23 0.37 0.23 0.23 0.76 0.24 0.30
NRN1L ENST00000339176 75.30 88.16 85.08 0.37 0.24 0.33 0.76 0.38 0.38
AATK ENST00000326724 75.30 17.27 44.95 0.37 1.61 0.68 0.75 0.75 2.04
SERPINB13 ENST00000344731 75.31 62.61 71.48 0.37 0.51 0.46 0.76 1.31 0.86
KRTAP1-4 ENST00000377747 75.31 75.11 78.45 0.37 0.51 0.38 0.76 0.91 0.54
CYP2D6 ENST00000360608 75.32 96.69 89.12 0.37 0.23 0.19 0.76 0.20 0.26
CIDEA ENST00000320477 75.32 86.00 83.95 0.37 0.27 0.35 0.75 0.43 0.43
TMEM171 ENST00000454765 75.33 91.94 86.78 0.37 0.23 0.30 0.75 0.33 0.31
RIN1 ENST00000311320 75.33 50.11 64.00 0.37 0.67 0.52 0.75 1.98 1.38
TREML1 ENST00000426005 75.34 90.72 86.26 0.37 0.25 0.33 0.75 0.35 0.33
RP1-127H14.3 ENST00000535109 75.34 90.60 86.19 0.37 0.25 0.33 0.75 0.37 0.33
IL16 ENST00000302987 75.35 36.70 55.70 0.37 0.77 0.53 0.75 1.66 1.73
NDOR1 ENST00000371521 75.35 59.46 69.60 0.37 0.51 0.44 0.75 1.41 0.95
ZNF234 ENST00000426739 75.36 69.29 75.22 0.37 0.57 0.37 0.75 1.14 0.67
NLRP14 ENST00000299481 75.36 79.83 80.95 0.37 0.35 0.39 0.75 0.62 0.50
PRRX2 ENST00000372469 75.37 60.16 70.01 0.37 0.52 0.47 0.75 1.38 0.91
SLIRP ENST00000557342 75.37 94.47 88.07 0.37 0.23 0.23 0.75 0.24 0.30
KLK10 ENST00000309958 75.38 82.30 82.21 0.37 0.34 0.35 0.75 0.53 0.44
SLC22A13 ENST00000311856 75.38 77.40 79.68 0.37 0.42 0.38 0.75 0.76 0.53
NEIL2 ENST00000284503 75.39 88.15 85.12 0.37 0.24 0.33 0.75 0.38 0.37
ZNF584 ENST00000306910 75.39 61.93 71.10 0.37 0.56 0.43 0.75 1.35 0.86
DUSP15 ENST00000339738 75.40 79.64 80.81 0.37 0.37 0.39 0.75 0.65 0.51
TAPBPL ENST00000266556 75.40 67.82 74.53 0.37 0.52 0.40 0.75 1.17 0.69
GGT1 ENST00000400382 75.41 36.34 55.54 0.37 0.82 0.52 0.75 1.62 1.74

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