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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
FAM194B ENST00000298738 98.65 59.53 82.46 0.10 0.49 0.33 0.11 1.41 0.44
SCGB2A1 ENST00000244930 99.92 75.19 90.63 0.10 0.49 0.15 0.14 0.91 0.20
LILRA4 ENST00000291759 97.39 77.06 90.26 0.10 0.42 0.16 0.11 0.78 0.22
PILRA ENST00000198536 98.66 86.43 95.27 0.10 0.24 0.08 0.11 0.42 0.10
TCEB3CL ENST00000451265 99.93 99.20 99.98 0.10 0.15 0.13 0.14 0.13 0.04
PIWIL3 ENST00000332271 97.39 67.01 85.56 0.10 0.53 0.33 0.11 1.24 0.35
ZNF749 ENST00000334181 98.66 85.46 94.78 0.10 0.25 0.09 0.11 0.45 0.11
ZNF17 ENST00000601808 97.40 78.53 90.97 0.10 0.40 0.15 0.11 0.74 0.20
RFPL4A ENST00000434937 99.93 87.56 96.55 0.10 0.23 0.07 0.14 0.37 0.07
CD300C ENST00000330793 98.67 80.98 92.57 0.10 0.35 0.14 0.11 0.56 0.15
NBPF10 ENST00000342960 97.40 97.32 99.16 0.10 0.23 0.11 0.11 0.19 0.04
KLRD1 ENST00000336164 99.94 65.89 86.15 0.10 0.54 0.33 0.14 1.23 0.33
SMIM21 ENST00000579022 98.67 95.29 98.96 0.10 0.23 0.10 0.11 0.21 0.04
MBL2 ENST00000373968 97.41 83.90 93.37 0.10 0.28 0.11 0.11 0.46 0.15
NLRP8 ENST00000291971 97.41 70.66 87.21 0.10 0.49 0.28 0.11 1.09 0.31
CEACAM1 ENST00000161559 98.68 39.17 71.42 0.10 0.70 0.46 0.11 1.61 0.87
CD58 ENST00000369489 99.94 34.44 69.32 0.10 0.80 0.43 0.14 1.56 0.98
SERPINA4 ENST00000557004 97.42 84.97 93.98 0.10 0.25 0.09 0.11 0.45 0.11
CXCL16 ENST00000293778 98.68 73.82 89.37 0.10 0.53 0.18 0.11 1.02 0.24
IL13 ENST00000304506 99.95 85.21 95.29 0.10 0.25 0.08 0.14 0.45 0.10
RNASE3 ENST00000304639 97.42 99.82 99.76 0.10 0.17 0.12 0.11 0.11 0.04
COX6C ENST00000520468 98.69 85.36 94.75 0.10 0.25 0.09 0.11 0.45 0.11
RHOXF2 ENST00000371388 97.43 94.48 98.26 0.10 0.23 0.09 0.11 0.24 0.05
C5orf60 ENST00000448248 99.95 85.06 95.24 0.10 0.25 0.08 0.14 0.45 0.10
FLG2 ENST00000388718 98.69 95.47 99.01 0.10 0.24 0.11 0.11 0.21 0.04

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