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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
HBQ1 ENST00000199708 86.59 94.78 93.42 0.24 0.23 0.11 0.41 0.24 0.15
MRPL28 ENST00000199706 79.75 81.37 83.91 0.33 0.33 0.35 0.58 0.54 0.43
EPDR1 ENST00000199448 64.61 60.15 63.56 0.56 0.52 0.49 1.19 1.39 1.39
NME8 ENST00000199447 69.80 72.98 74.26 0.52 0.51 0.39 0.95 1.03 0.69
EIF2AK1 ENST00000199389 50.31 37.05 41.90 0.57 0.78 0.68 1.81 1.68 2.01
DIMT1 ENST00000199320 23.53 53.46 36.61 1.38 0.65 0.85 1.08 1.72 1.93
AQP2 ENST00000199280 42.39 82.02 63.33 0.76 0.34 0.48 1.75 0.50 1.36
MOGAT2 ENST00000198801 65.43 41.13 52.58 0.56 0.59 0.61 1.12 1.82 1.89
RRN3 ENST00000198767 53.69 33.97 42.04 0.63 0.84 0.70 1.77 1.55 1.98
PILRA ENST00000198536 98.66 86.43 95.27 0.10 0.24 0.08 0.11 0.42 0.10
KIAA1467 ENST00000197268 42.80 26.22 32.70 0.78 1.19 0.86 1.77 1.08 1.63
ZNF8 ENST00000196548 47.68 37.49 40.76 0.53 0.78 0.81 1.80 1.67 2.04
ZNF416 ENST00000196489 95.42 56.71 79.36 0.11 0.53 0.39 0.11 1.56 0.54
OXCT1 ENST00000196371 9.91 28.09 16.83 2.09 1.19 1.70 0.50 1.20 0.70
PLOD1 ENST00000196061 45.49 48.91 45.89 0.57 0.63 0.70 1.75 2.04 1.98
C4orf6 ENST00000195455 97.79 97.44 99.29 0.11 0.22 0.11 0.11 0.19 0.04
STRADB ENST00000194530 17.52 35.45 24.56 1.47 0.77 1.06 0.88 1.56 1.09
HSPB11 ENST00000194214 29.51 73.45 50.50 1.08 0.53 0.67 1.55 1.03 1.86
PCDHB2 ENST00000194155 65.77 62.35 65.65 0.58 0.53 0.51 1.06 1.33 1.29
PCDHB4 ENST00000194152 66.05 74.43 72.99 0.59 0.53 0.40 1.05 1.00 0.80
SLC13A1 ENST00000194130 43.40 68.24 55.48 0.81 0.52 0.51 1.79 1.21 1.73
IMPG2 ENST00000193391 50.51 36.92 41.96 0.58 0.76 0.68 1.80 1.70 2.01
OSTM1 ENST00000193322 5.49 33.76 17.48 3.33 0.85 1.62 0.33 1.56 0.75
UHRF1BP1 ENST00000192788 36.54 33.04 32.96 0.95 0.85 0.86 1.78 1.49 1.67
GAL3ST2 ENST00000192314 87.00 93.15 92.79 0.23 0.28 0.14 0.39 0.30 0.15

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