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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
HAO1 ENST00000378789 52.56 64.61 58.67 0.67 0.48 0.52 1.80 1.22 1.65
GYG1 ENST00000345003 52.56 74.57 65.01 0.67 0.52 0.51 1.80 1.00 1.31
FAM104A ENST00000405159 52.57 44.74 47.43 0.68 0.66 0.63 1.79 1.98 1.88
ARSG ENST00000448504 52.57 64.45 58.59 0.68 0.48 0.51 1.79 1.21 1.65
INSM2 ENST00000307169 52.58 20.04 34.54 0.68 1.43 0.90 1.79 0.73 1.78
MEI1 ENST00000401548 52.59 33.47 41.24 0.68 0.84 0.75 1.79 1.52 2.01
ECSIT ENST00000270517 52.59 54.70 53.06 0.70 0.58 0.61 1.79 1.65 1.87
TTC9B ENST00000311308 52.60 49.34 49.96 0.70 0.65 0.61 1.79 2.02 1.90
CLTCL1 ENST00000263200 52.60 52.59 51.75 0.70 0.67 0.62 1.79 1.82 1.93
INA ENST00000369849 52.61 73.99 64.65 0.70 0.53 0.51 1.78 1.02 1.32
TNFRSF11A ENST00000586569 52.61 29.87 39.60 0.70 1.14 0.80 1.78 1.40 2.04
C11orf84 ENST00000294244 52.62 6.38 27.64 0.70 2.66 0.96 1.78 0.37 1.27
PLEC ENST00000322810 52.62 17.17 33.05 0.70 1.61 0.85 1.78 0.75 1.67
FANCL ENST00000402135 52.63 82.60 69.84 0.70 0.34 0.46 1.78 0.51 0.93
GLB1 ENST00000307363 52.63 46.65 48.54 0.70 0.75 0.68 1.78 1.97 1.85
PARS2 ENST00000371279 52.64 49.39 50.01 0.70 0.65 0.61 1.78 2.01 1.92
INHBC ENST00000309668 52.64 66.38 59.93 0.70 0.54 0.49 1.78 1.20 1.63
EXOSC4 ENST00000316052 52.65 60.68 56.48 0.70 0.54 0.52 1.78 1.40 1.70
CCDC67 ENST00000298050 52.65 56.33 54.01 0.70 0.52 0.59 1.78 1.54 1.77
LRP10 ENST00000359591 52.66 48.09 49.26 0.70 0.63 0.71 1.77 1.99 1.85
SHCBP1 ENST00000303383 52.66 40.88 45.50 0.70 0.61 0.70 1.77 1.78 1.97
HFE2 ENST00000336751 52.67 45.36 47.85 0.68 0.68 0.65 1.77 1.99 1.89
SNN ENST00000329565 52.67 89.06 73.65 0.68 0.27 0.40 1.77 0.35 0.74
PSMD9 ENST00000541212 52.68 77.29 66.70 0.68 0.42 0.54 1.77 0.77 1.20
USE1 ENST00000263897 52.68 57.76 54.80 0.68 0.57 0.53 1.77 1.47 1.73

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