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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
ABT1 ENST00000274849 62.50 57.74 60.67 0.65 0.57 0.44 1.28 1.47 1.61
OR10K1 ENST00000289451 62.51 65.25 65.43 0.63 0.51 0.53 1.28 1.24 1.31
CCDC53 ENST00000240079 62.51 52.63 57.52 0.62 0.68 0.52 1.28 1.81 1.66
OR13J1 ENST00000377981 62.52 94.08 81.69 0.62 0.25 0.37 1.28 0.26 0.47
LRRC3 ENST00000291592 62.52 85.79 77.32 0.62 0.28 0.35 1.28 0.44 0.58
DAPP1 ENST00000512369 62.53 26.35 42.77 0.62 1.19 0.70 1.27 1.08 2.02
EPGN ENST00000413830 62.53 83.14 75.85 0.62 0.29 0.38 1.27 0.49 0.63
UROC1 ENST00000383579 62.54 53.30 57.97 0.62 0.66 0.47 1.27 1.72 1.68
COMMD7 ENST00000278980 62.54 73.73 70.45 0.62 0.52 0.43 1.27 1.03 0.91
NIF3L1 ENST00000409020 62.55 69.63 68.04 0.62 0.53 0.51 1.27 1.11 1.10
HCAR2 ENST00000328880 62.55 83.84 76.29 0.62 0.28 0.37 1.27 0.47 0.61
FAHD2A ENST00000233379 62.56 65.89 65.84 0.62 0.54 0.51 1.27 1.22 1.25
MAP4 ENST00000360240 62.56 15.68 37.37 0.62 1.87 0.85 1.27 0.68 2.01
CXCL11 ENST00000306621 62.57 61.14 62.86 0.62 0.53 0.51 1.27 1.40 1.40
IP6K3 ENST00000451316 62.57 67.65 66.84 0.61 0.53 0.53 1.28 1.19 1.19
FAM46B ENST00000289166 62.58 38.27 49.31 0.61 0.75 0.70 1.28 1.70 1.85
WTIP ENST00000590071 62.58 54.27 58.49 0.61 0.62 0.51 1.28 1.69 1.64
FOXR1 ENST00000317011 62.59 68.05 67.06 0.61 0.52 0.52 1.28 1.19 1.16
ALKBH3 ENST00000302708 62.59 74.85 71.18 0.59 0.53 0.44 1.28 0.95 0.86
KAL1 ENST00000262648 62.60 10.65 34.81 0.59 2.14 0.90 1.28 0.51 1.76
MARVELD3 ENST00000299952 62.61 67.53 66.78 0.59 0.54 0.53 1.28 1.20 1.20
VAX1 ENST00000369206 62.61 25.56 42.35 0.59 1.25 0.68 1.28 1.05 2.02
B4GALNT3 ENST00000266383 62.62 40.65 50.70 0.59 0.63 0.66 1.28 1.77 1.84
HSD17B8 ENST00000374662 62.62 57.71 60.78 0.59 0.57 0.44 1.28 1.47 1.61
RAB32 ENST00000367495 62.63 70.68 68.66 0.59 0.49 0.47 1.29 1.09 1.05

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