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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
CHKB ENST00000406938 55.01 50.58 52.02 0.62 0.63 0.62 1.69 1.94 1.94
SPINK5 ENST00000359874 55.02 49.95 51.64 0.62 0.66 0.62 1.70 2.02 1.92
GOLGA2 ENST00000421699 55.02 12.72 32.06 0.62 2.09 0.90 1.70 0.59 1.60
NARF ENST00000309794 55.03 67.99 62.34 0.62 0.52 0.48 1.69 1.19 1.41
BSX ENST00000343035 55.03 64.15 60.02 0.62 0.49 0.48 1.69 1.21 1.62
PLIN2 ENST00000276914 55.04 70.51 64.04 0.62 0.52 0.53 1.69 1.08 1.39
SRBD1 ENST00000263736 55.04 53.53 53.71 0.62 0.65 0.62 1.69 1.70 1.81
KIRREL2 ENST00000360202 55.05 47.41 50.26 0.62 0.66 0.65 1.69 2.01 1.92
MATK ENST00000395045 55.05 40.76 46.59 0.62 0.62 0.66 1.68 1.78 1.89
TMEM260 ENST00000261556 55.06 62.74 59.04 0.62 0.51 0.49 1.68 1.31 1.66
BDH1 ENST00000392379 55.06 78.26 68.67 0.62 0.43 0.47 1.68 0.74 1.05
NOD2 ENST00000300589 55.07 74.61 66.50 0.62 0.53 0.51 1.69 0.99 1.21
UBXN2A ENST00000309033 55.07 75.98 67.33 0.62 0.43 0.52 1.69 0.86 1.15
MRPS21 ENST00000369084 55.08 81.83 70.79 0.62 0.35 0.43 1.70 0.51 0.86
MYL9 ENST00000279022 55.08 80.55 70.06 0.62 0.37 0.47 1.70 0.58 0.91
IGFBP4 ENST00000269593 55.09 53.72 53.86 0.62 0.63 0.61 1.69 1.70 1.78
SLC39A5 ENST00000266980 55.10 64.88 60.52 0.62 0.48 0.44 1.70 1.24 1.58
METTL21A ENST00000411432 55.10 74.30 66.40 0.62 0.53 0.52 1.70 1.01 1.20
DOCK6 ENST00000294618 55.11 37.74 45.09 0.62 0.80 0.70 1.70 1.70 2.02
FAM160B2 ENST00000289921 55.11 40.15 46.28 0.62 0.62 0.67 1.70 1.72 1.92
HYKK ENST00000388988 55.12 62.15 58.73 0.62 0.53 0.52 1.70 1.35 1.65
RGS16 ENST00000367558 55.12 82.26 71.17 0.62 0.34 0.44 1.70 0.52 0.86
SEMA4A ENST00000368285 55.13 33.39 42.51 0.62 0.84 0.68 1.70 1.51 2.01
ACOT12 ENST00000307624 55.13 57.96 56.30 0.62 0.56 0.49 1.69 1.46 1.75
GHITM ENST00000372134 55.14 33.97 42.88 0.62 0.84 0.67 1.69 1.55 1.99

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