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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
CDK3 ENST00000425876 19.12 67.70 41.64 1.58 0.53 0.72 0.95 1.19 2.02
AICDA ENST00000229335 19.12 67.63 41.60 1.58 0.53 0.72 0.95 1.19 1.99
EEF1G ENST00000329251 19.13 5.29 9.69 1.58 3.11 2.26 0.95 0.32 0.40
KMT2E ENST00000311117 19.13 0.24 7.03 1.58 4.11 2.90 0.95 0.28 0.33
INTS8 ENST00000523731 19.14 13.45 13.98 1.58 2.05 2.05 0.95 0.60 0.59
FUT9 ENST00000302103 19.14 36.70 26.09 1.58 0.77 0.99 0.95 1.66 1.25
SRGAP3 ENST00000383836 19.15 8.20 11.35 1.58 2.57 2.20 0.95 0.44 0.45
DENND4B ENST00000361217 19.15 12.07 13.22 1.58 2.06 2.09 0.95 0.57 0.53
RABGAP1L ENST00000251507 19.16 25.16 20.23 1.58 1.32 1.48 0.95 1.03 0.88
DMXL2 ENST00000543779 19.16 2.61 8.24 1.58 3.54 2.57 0.95 0.29 0.37
ABCC8 ENST00000389817 19.17 40.54 28.04 1.58 0.63 0.82 0.94 1.77 1.28
INS-IGF2 ENST00000397270 19.17 58.65 37.16 1.58 0.54 0.81 0.94 1.42 1.97
GTSF1 ENST00000552397 19.18 40.03 27.76 1.58 0.63 0.90 0.94 1.68 1.27
CANX ENST00000247461 19.18 13.51 14.03 1.58 2.06 2.04 0.94 0.61 0.60
UBE3C ENST00000348165 19.19 5.12 9.62 1.58 3.20 2.26 0.94 0.33 0.40
EIF2B4 ENST00000451130 19.19 14.32 14.49 1.57 2.04 2.00 0.94 0.61 0.59
EBP ENST00000495186 19.20 14.37 14.50 1.57 2.04 2.00 0.94 0.61 0.59
NSF ENST00000398238 19.20 31.52 23.48 1.57 0.96 1.18 0.94 1.41 1.00
PPP1R11 ENST00000376772 19.21 55.17 35.40 1.57 0.57 0.87 0.94 1.61 1.76
ALDH1A3 ENST00000329841 19.21 25.43 20.39 1.57 1.25 1.49 0.94 1.05 0.88
ZKSCAN1 ENST00000324306 19.22 13.94 14.30 1.57 2.05 2.01 0.94 0.60 0.60
SYNRG ENST00000339208 19.22 13.72 14.19 1.57 2.06 1.99 0.94 0.60 0.60
CDK14 ENST00000265741 19.23 54.18 34.87 1.56 0.63 0.90 0.94 1.69 1.75
IGF1R ENST00000268035 19.23 11.92 13.17 1.56 2.09 2.10 0.95 0.59 0.52
MAT1A ENST00000372213 19.24 40.01 27.78 1.56 0.63 0.90 0.95 1.69 1.27

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