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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
COPZ2 ENST00000006101 71.78 84.37 81.42 0.34 0.29 0.37 0.83 0.44 0.48
TRAPPC6A ENST00000006275 78.77 94.41 89.70 0.35 0.23 0.18 0.65 0.24 0.23
SPATA20 ENST00000006658 53.53 37.01 43.62 0.62 0.77 0.59 1.76 1.68 2.01
CEACAM7 ENST00000006724 95.68 79.45 90.64 0.11 0.38 0.15 0.12 0.67 0.20
RHBDD2 ENST00000006777 49.46 27.61 36.69 0.56 1.27 0.82 1.80 1.17 1.93
TSR3 ENST00000007390 85.36 64.38 78.11 0.28 0.49 0.39 0.47 1.22 0.55
OSBPL7 ENST00000007414 28.10 22.76 23.52 1.16 1.46 1.18 1.48 0.89 1.00
YBX2 ENST00000007699 7.90 3.10 2.89 2.67 3.45 4.01 0.41 0.28 0.23
ITGA3 ENST00000007722 31.47 26.63 27.20 0.94 1.20 0.99 1.68 1.12 1.25
KRT33A ENST00000007735 63.50 86.86 78.43 0.59 0.22 0.38 1.24 0.40 0.54
LRRC23 ENST00000007969 40.00 68.09 53.46 0.86 0.52 0.62 1.76 1.20 1.83
TFAP2D ENST00000008391 15.12 8.78 9.40 1.57 2.47 2.29 0.74 0.48 0.39
CRY1 ENST00000008527 21.20 43.13 30.36 1.52 0.62 0.81 1.03 1.89 1.45
PGLYRP1 ENST00000008938 87.09 89.74 91.33 0.23 0.27 0.15 0.38 0.37 0.18
STARD3NL ENST00000009041 16.67 44.67 28.82 1.44 0.66 0.80 0.83 1.97 1.31
CAMK1G ENST00000009105 20.52 36.11 26.40 1.54 0.81 1.01 1.01 1.59 1.25
CD74 ENST00000009530 39.76 28.81 32.47 0.89 1.14 0.89 1.73 1.30 1.63
FAM76A ENST00000010299 19.07 40.57 28.02 1.58 0.63 0.82 0.95 1.76 1.27
CPA1 ENST00000011292 44.93 70.87 57.94 0.63 0.49 0.48 1.74 1.07 1.66
SYPL1 ENST00000011473 39.11 43.78 39.80 0.90 0.61 0.80 1.77 1.96 2.02
RANBP9 ENST00000011619 6.40 0.62 1.51 3.04 4.14 4.33 0.36 0.28 0.22
CD4 ENST00000011653 99.91 39.67 72.48 0.10 0.68 0.44 0.14 1.66 0.83
TSPAN9 ENST00000011898 28.14 25.38 24.80 1.16 1.27 1.04 1.47 1.04 1.11
QPCTL ENST00000012049 57.46 75.56 68.50 0.58 0.44 0.47 1.54 0.90 1.06
PPP5C ENST00000012443 11.71 6.30 6.32 1.67 2.69 3.11 0.59 0.36 0.32

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