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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
CLDN14 ENST00000399137 54.24 87.66 73.77 0.63 0.24 0.42 1.73 0.36 0.71
ZNF484 ENST00000395506 54.24 49.01 50.66 0.63 0.66 0.66 1.73 2.03 1.85
EPHX2 ENST00000521400 54.25 69.99 63.20 0.63 0.53 0.49 1.74 1.14 1.37
FKBP11 ENST00000550765 54.25 83.51 71.39 0.63 0.27 0.44 1.74 0.47 0.86
EXOG ENST00000287675 54.26 82.21 70.54 0.65 0.34 0.43 1.73 0.52 0.91
ALG3 ENST00000397676 54.26 69.12 62.59 0.65 0.56 0.48 1.73 1.12 1.40
NCAPD3 ENST00000534548 54.27 24.60 37.67 0.65 1.30 0.82 1.72 1.05 2.01
DNMBP ENST00000324109 54.27 37.08 44.11 0.65 0.78 0.61 1.72 1.66 2.03
KLHL29 ENST00000486442 54.28 13.16 31.92 0.65 2.05 0.91 1.72 0.60 1.57
BST1 ENST00000265016 54.28 71.75 64.29 0.65 0.51 0.51 1.72 1.08 1.35
LPIN1 ENST00000449576 54.29 40.00 45.84 0.65 0.63 0.68 1.73 1.68 1.97
MSMP ENST00000436428 54.29 60.86 57.54 0.65 0.56 0.52 1.73 1.41 1.66
CRIP3 ENST00000372569 54.30 56.64 55.04 0.65 0.53 0.51 1.73 1.55 1.74
SLC14A2 ENST00000255226 54.31 53.34 53.24 0.65 0.66 0.61 1.73 1.70 1.89
CLCC1 ENST00000369971 54.31 29.68 40.26 0.65 1.13 0.80 1.73 1.39 2.00
CCR8 ENST00000326306 54.32 72.08 64.52 0.65 0.52 0.51 1.73 1.03 1.34
GEMIN4 ENST00000319004 54.32 55.66 54.55 0.65 0.52 0.56 1.73 1.60 1.74
PM20D1 ENST00000367136 54.33 74.53 66.05 0.65 0.53 0.51 1.73 1.00 1.23
ZNF713 ENST00000429591 54.33 52.96 53.07 0.65 0.63 0.62 1.73 1.78 1.87
MCM3AP ENST00000397708 54.34 24.69 37.74 0.65 1.29 0.84 1.73 1.04 2.01
GJB5 ENST00000338513 54.34 90.56 75.37 0.65 0.25 0.37 1.73 0.37 0.66
ACSS3 ENST00000548058 54.35 48.95 50.72 0.65 0.65 0.66 1.73 2.04 1.84
INHA ENST00000243786 54.35 56.92 55.22 0.65 0.56 0.51 1.73 1.53 1.74
S100PBP ENST00000373475 54.36 15.09 32.90 0.65 1.91 0.86 1.73 0.65 1.67
SMYD3 ENST00000388985 54.36 52.11 52.54 0.65 0.61 0.61 1.73 1.85 1.90

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