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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
CD36 ENST00000435819 81.48 97.51 92.16 0.33 0.22 0.14 0.60 0.19 0.16
GAB4 ENST00000400588 81.49 69.86 78.95 0.33 0.54 0.39 0.60 1.14 0.52
HAMP ENST00000598398 81.49 89.94 88.83 0.33 0.25 0.19 0.60 0.37 0.28
BCL2L12 ENST00000246785 81.50 74.81 81.50 0.33 0.53 0.35 0.60 0.95 0.48
KRTAP21-1 ENST00000335093 81.50 89.49 88.64 0.33 0.27 0.20 0.60 0.36 0.28
AC011897.1 ENST00000581929 81.51 84.00 86.00 0.33 0.27 0.33 0.60 0.46 0.33
TBCA ENST00000380377 81.51 60.73 73.90 0.33 0.56 0.40 0.59 1.40 0.70
DOK2 ENST00000276420 81.52 51.46 68.47 0.33 0.63 0.47 0.59 1.89 1.06
KLHL35 ENST00000539798 81.52 92.38 90.02 0.33 0.25 0.18 0.59 0.30 0.22
C17orf47 ENST00000321691 81.53 46.26 65.44 0.32 0.73 0.52 0.59 2.04 1.31
MBLAC1 ENST00000398075 81.54 82.77 85.51 0.32 0.33 0.33 0.59 0.50 0.35
RP11-113D6.6 ENST00000527671 81.54 91.33 89.57 0.32 0.23 0.18 0.59 0.34 0.23
CA4 ENST00000300900 81.55 66.70 77.29 0.30 0.56 0.35 0.59 1.22 0.58
PPP1R3F ENST00000055335 81.55 75.26 81.79 0.30 0.49 0.37 0.59 0.90 0.47
TFPI2 ENST00000222543 81.56 68.96 78.47 0.30 0.54 0.38 0.60 1.16 0.54
BPIFA3 ENST00000375454 81.56 89.67 88.75 0.30 0.27 0.19 0.60 0.36 0.28
REXO4 ENST00000371942 81.57 61.32 74.32 0.30 0.54 0.40 0.60 1.39 0.69
KRTAP6-3 ENST00000391624 81.57 74.84 81.57 0.30 0.53 0.35 0.60 0.95 0.47
CD207 ENST00000410009 81.58 76.37 82.36 0.30 0.43 0.33 0.60 0.86 0.44
RP11-332O19.5 ENST00000441178 81.58 86.98 87.45 0.30 0.22 0.28 0.60 0.40 0.30
OVCA2 ENST00000572195 81.59 93.47 90.59 0.30 0.28 0.15 0.60 0.28 0.20
KLRG2 ENST00000340940 81.59 85.39 86.67 0.30 0.25 0.30 0.60 0.45 0.33
C9orf131 ENST00000312292 81.60 74.22 81.26 0.30 0.53 0.38 0.60 1.02 0.48
CLEC14A ENST00000342213 81.60 67.95 77.99 0.30 0.52 0.38 0.60 1.17 0.54
UTS2B ENST00000340524 81.61 83.47 85.84 0.30 0.27 0.33 0.60 0.46 0.33

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