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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
USP10 ENST00000219473 50.11 6.22 26.28 0.57 2.73 1.01 1.80 0.36 1.25
CCNH ENST00000256897 50.11 43.49 45.51 0.57 0.61 0.70 1.80 1.96 1.97
SLC37A3 ENST00000326232 50.12 57.68 53.31 0.57 0.56 0.62 1.80 1.48 1.85
SGCG ENST00000218867 50.12 57.19 53.08 0.57 0.56 0.61 1.80 1.48 1.87
SPATA13 ENST00000424834 50.13 24.12 35.33 0.57 1.35 0.87 1.80 0.98 1.76
SLC7A6OS ENST00000263997 50.13 31.01 38.90 0.57 1.05 0.80 1.80 1.36 2.06
AP1S3 ENST00000396654 50.14 62.48 56.00 0.57 0.53 0.49 1.80 1.31 1.77
XYLT1 ENST00000261381 50.14 14.64 30.66 0.57 2.01 0.80 1.80 0.61 1.47
KIAA0391 ENST00000534898 50.15 68.82 59.89 0.57 0.53 0.49 1.80 1.19 1.63
CSTA ENST00000264474 50.15 95.10 75.61 0.57 0.23 0.38 1.80 0.21 0.64
SLC26A7 ENST00000309536 50.16 43.17 45.37 0.57 0.62 0.70 1.80 1.91 2.00
TNS4 ENST00000254051 50.16 39.50 43.20 0.57 0.70 0.65 1.80 1.63 1.99
MSX2 ENST00000239243 50.17 50.84 49.40 0.57 0.63 0.70 1.80 1.92 1.83
TJAP1 ENST00000372445 50.17 47.37 47.54 0.57 0.66 0.63 1.80 2.01 1.89
AFAP1L1 ENST00000296721 50.18 52.20 50.23 0.57 0.62 0.65 1.80 1.84 1.90
LTBP2 ENST00000261978 50.18 16.82 31.70 0.57 1.67 0.89 1.80 0.71 1.58
BFAR ENST00000261658 50.19 52.12 50.17 0.57 0.61 0.63 1.80 1.85 1.90
CCDC38 ENST00000344280 50.19 58.72 53.95 0.57 0.54 0.61 1.80 1.43 1.77
C1orf85 ENST00000362007 50.20 76.96 65.04 0.57 0.43 0.51 1.80 0.79 1.31
SLC25A15 ENST00000338625 50.20 73.07 62.50 0.57 0.53 0.48 1.80 1.02 1.40
TACR2 ENST00000373306 50.21 60.40 54.85 0.57 0.53 0.52 1.80 1.41 1.74
CCDC155 ENST00000447857 50.21 40.71 43.80 0.57 0.63 0.61 1.80 1.78 2.01
GGH ENST00000260118 50.22 25.29 35.84 0.57 1.28 0.86 1.80 1.03 1.79
ZNF740 ENST00000416904 50.22 23.19 34.88 0.57 1.44 0.90 1.80 0.91 1.75
ARHGAP33 ENST00000314737 50.23 18.28 32.45 0.57 1.49 0.90 1.80 0.74 1.61

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