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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
SGOL1 ENST00000263753 60.44 69.04 66.43 0.58 0.54 0.51 1.37 1.14 1.22
TMEM174 ENST00000296776 60.44 53.60 56.87 0.58 0.62 0.51 1.37 1.72 1.70
HSD17B13 ENST00000328546 60.45 61.77 61.87 0.58 0.57 0.47 1.38 1.37 1.46
PSMG3 ENST00000288607 60.45 83.91 75.12 0.58 0.28 0.39 1.38 0.46 0.67
PSAP ENST00000394936 60.46 11.18 33.98 0.58 2.09 0.90 1.38 0.54 1.73
DGUOK ENST00000264093 60.46 66.31 64.77 0.58 0.54 0.49 1.38 1.20 1.32
FMO6P ENST00000236166 60.47 59.87 60.75 0.58 0.52 0.44 1.37 1.36 1.61
ZCCHC12 ENST00000310164 60.47 59.58 60.54 0.58 0.52 0.44 1.37 1.41 1.58
CYP2J2 ENST00000371204 60.48 75.15 70.04 0.58 0.51 0.47 1.37 0.91 0.91
NSG1 ENST00000421177 60.48 73.58 69.11 0.58 0.52 0.44 1.37 1.03 1.00
IL1RN ENST00000259206 60.49 48.47 53.96 0.58 0.65 0.61 1.37 2.02 1.77
CTSC ENST00000227266 60.49 57.80 59.38 0.58 0.57 0.49 1.37 1.47 1.70
HAUS1 ENST00000282058 60.50 73.69 69.20 0.58 0.52 0.44 1.37 1.03 0.99
SLC15A3 ENST00000227880 60.50 77.63 71.60 0.58 0.42 0.44 1.36 0.79 0.83
RP1 ENST00000220676 60.51 36.95 47.49 0.58 0.75 0.63 1.36 1.70 1.89
KIAA1430 ENST00000458385 60.51 51.05 55.45 0.58 0.65 0.51 1.36 1.92 1.72
KDELR3 ENST00000409006 60.52 96.06 81.68 0.58 0.21 0.37 1.36 0.20 0.47
STX8 ENST00000306357 60.52 68.20 66.00 0.57 0.52 0.51 1.36 1.21 1.22
MTMR9 ENST00000221086 60.53 29.57 43.40 0.57 1.10 0.63 1.36 1.39 2.00
MOCOS ENST00000261326 60.53 63.52 63.11 0.57 0.49 0.49 1.36 1.25 1.39
CEBPZ ENST00000234170 60.54 28.71 42.94 0.58 1.15 0.67 1.36 1.29 2.00
CATSPERG ENST00000409235 60.54 47.06 53.23 0.58 0.67 0.61 1.36 1.99 1.88
PCDHA3 ENST00000522353 60.55 71.68 68.09 0.58 0.52 0.51 1.35 1.07 1.10
NABP1 ENST00000425611 60.55 68.49 66.21 0.58 0.52 0.52 1.35 1.20 1.20
PTOV1 ENST00000391842 60.56 18.70 37.90 0.58 1.53 0.85 1.35 0.75 2.01

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