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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
F2RL2 ENST00000296641 49.85 80.04 66.65 0.54 0.37 0.52 1.82 0.60 1.20
PPAPDC3 ENST00000372264 49.85 74.59 63.34 0.54 0.53 0.48 1.82 1.00 1.36
PRNP ENST00000379440 49.86 70.01 60.43 0.54 0.53 0.44 1.82 1.13 1.58
TYW3 ENST00000370867 49.86 59.56 54.26 0.54 0.52 0.59 1.82 1.41 1.73
BBOX1 ENST00000263182 49.87 78.29 65.68 0.54 0.43 0.51 1.82 0.74 1.27
ICOS ENST00000316386 49.87 49.99 48.82 0.54 0.66 0.70 1.82 2.01 1.86
TCEAL7 ENST00000332431 49.88 76.51 64.52 0.54 0.42 0.51 1.82 0.83 1.34
LRRC14 ENST00000292524 49.88 54.54 51.29 0.53 0.59 0.63 1.82 1.66 1.92
DPYS ENST00000351513 49.89 62.81 56.06 0.53 0.51 0.49 1.82 1.30 1.76
GJB6 ENST00000356192 49.89 89.39 72.33 0.53 0.27 0.44 1.81 0.37 0.82
MICALL1 ENST00000215957 49.90 38.98 42.77 0.53 0.70 0.70 1.81 1.65 2.01
CNIH4 ENST00000465271 49.90 53.87 50.95 0.53 0.63 0.66 1.81 1.70 1.85
GZF1 ENST00000338121 49.91 30.46 38.47 0.53 1.09 0.84 1.81 1.38 2.05
CNTROB ENST00000380262 49.91 42.54 44.88 0.53 0.59 0.68 1.81 1.88 2.04
NT5C1B-RDH14 ENST00000532967 49.92 49.01 48.33 0.53 0.66 0.67 1.80 2.03 1.88
TLR4 ENST00000355622 49.93 53.69 50.88 0.53 0.63 0.67 1.80 1.69 1.85
ZBTB49 ENST00000337872 49.93 47.50 47.48 0.54 0.62 0.63 1.80 2.01 1.89
CALCB ENST00000533448 49.94 70.08 60.53 0.54 0.53 0.44 1.80 1.13 1.58
FAM96A ENST00000300030 49.94 79.27 66.29 0.54 0.38 0.52 1.80 0.67 1.21
IGDCC3 ENST00000327987 49.95 41.92 44.43 0.54 0.61 0.61 1.80 1.82 2.04
ELP4 ENST00000350638 49.95 58.38 53.58 0.54 0.54 0.63 1.80 1.41 1.80
COL27A1 ENST00000356083 49.96 12.69 29.50 0.54 2.10 0.84 1.80 0.58 1.38
HPGD ENST00000296522 49.96 69.18 59.98 0.54 0.56 0.48 1.80 1.12 1.62
PSTPIP1 ENST00000558012 49.97 38.31 42.42 0.54 0.75 0.68 1.80 1.71 2.01
SFTPD ENST00000372292 49.97 52.85 50.43 0.54 0.65 0.67 1.80 1.80 1.89

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