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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
TUSC3 ENST00000503731 40.68 51.12 44.38 0.86 0.66 0.62 1.74 1.91 2.03
TMEM86A ENST00000280734 40.68 56.66 47.44 0.86 0.53 0.63 1.74 1.55 1.87
CD2AP ENST00000359314 40.69 18.95 28.00 0.86 1.52 0.82 1.74 0.76 1.27
MORN4 ENST00000307450 40.70 38.12 37.65 0.86 0.77 0.82 1.74 1.71 2.00
EXO5 ENST00000372703 40.70 75.22 58.02 0.87 0.49 0.47 1.74 0.90 1.66
DIO1 ENST00000361921 40.71 31.46 34.37 0.87 0.96 0.87 1.74 1.42 1.77
RAB34 ENST00000447716 40.71 55.48 46.83 0.87 0.57 0.67 1.74 1.60 1.88
NECAB3 ENST00000246190 40.72 44.60 40.83 0.87 0.65 0.80 1.74 1.97 2.04
SPATS2L ENST00000358677 40.72 20.87 28.94 0.87 1.42 0.81 1.74 0.84 1.31
RMND1 ENST00000367303 40.73 65.33 52.29 0.87 0.51 0.59 1.74 1.25 1.90
CCDC158 ENST00000388914 40.73 52.36 45.24 0.87 0.62 0.70 1.74 1.82 2.00
C14orf119 ENST00000319074 40.74 76.26 58.57 0.87 0.44 0.51 1.75 0.86 1.65
TAF1A ENST00000350027 40.74 54.51 46.33 0.87 0.59 0.67 1.75 1.66 1.90
PKP1 ENST00000263946 40.75 27.43 32.29 0.87 1.25 0.90 1.75 1.17 1.60
HARS2 ENST00000230771 40.75 40.30 38.83 0.87 0.62 0.82 1.75 1.75 2.04
IL23R ENST00000347310 40.76 30.65 33.86 0.87 1.06 0.89 1.75 1.37 1.72
SCCPDH ENST00000366510 40.76 58.86 48.69 0.87 0.53 0.68 1.75 1.41 1.85
PACSIN3 ENST00000539589 40.77 31.55 34.41 0.86 0.95 0.90 1.75 1.43 1.76
BAIAP2 ENST00000321300 40.77 21.61 29.36 0.86 1.44 0.82 1.75 0.81 1.35
P4HA3 ENST00000331597 40.78 52.20 45.14 0.86 0.62 0.70 1.75 1.84 2.00
XRCC6BP1 ENST00000300145 40.78 71.01 55.58 0.86 0.49 0.53 1.75 1.07 1.73
GUSB ENST00000304895 40.79 40.00 38.63 0.86 0.63 0.84 1.75 1.69 2.01
GPR158 ENST00000376351 40.79 23.53 30.33 0.86 1.39 0.84 1.75 0.92 1.45
FOXA1 ENST00000250448 40.80 34.86 35.95 0.86 0.76 0.86 1.75 1.55 1.78
DHX35 ENST00000252011 40.80 60.96 49.87 0.86 0.54 0.63 1.75 1.41 1.89

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