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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
AMZ1 ENST00000312371 85.49 95.40 93.19 0.28 0.24 0.14 0.47 0.21 0.15
CYP4A22 ENST00000371891 85.49 93.49 92.15 0.28 0.28 0.14 0.47 0.28 0.16
IFIT1B ENST00000371809 85.50 93.97 92.43 0.28 0.25 0.14 0.47 0.26 0.15
FANCA ENST00000389301 85.50 76.18 84.10 0.28 0.43 0.34 0.47 0.86 0.42
KRTAP5-11 ENST00000398530 85.51 87.95 89.82 0.28 0.25 0.18 0.47 0.37 0.23
S100P ENST00000296370 85.51 89.80 90.74 0.28 0.27 0.15 0.47 0.37 0.20
CYP2C8 ENST00000371270 85.52 93.42 92.12 0.28 0.28 0.14 0.47 0.28 0.16
DEFB110 ENST00000371148 85.52 94.95 92.99 0.28 0.23 0.14 0.47 0.21 0.15
APBA3 ENST00000316757 85.53 69.14 80.65 0.28 0.56 0.39 0.47 1.12 0.51
TMEM92 ENST00000300433 85.53 75.25 83.78 0.28 0.49 0.34 0.47 0.90 0.41
CTSG ENST00000216336 85.54 74.37 83.31 0.28 0.53 0.32 0.46 1.00 0.40
C1orf173 ENST00000326665 85.54 71.33 81.80 0.28 0.53 0.37 0.46 1.06 0.47
CCDC74A ENST00000295171 85.55 91.16 91.28 0.28 0.24 0.15 0.46 0.35 0.18
HDHD1 ENST00000424830 85.55 47.45 68.47 0.28 0.65 0.47 0.46 2.02 1.06
ICAM4 ENST00000340992 85.56 87.47 89.65 0.28 0.23 0.18 0.46 0.39 0.23
DRD4 ENST00000176183 85.56 93.12 92.05 0.28 0.28 0.14 0.46 0.30 0.16
ZNF831 ENST00000371030 85.57 38.57 63.15 0.28 0.72 0.49 0.46 1.67 1.37
EBI3 ENST00000221847 85.57 46.10 67.68 0.28 0.75 0.52 0.46 2.03 1.13
PODNL1 ENST00000339560 85.58 83.32 87.59 0.28 0.27 0.27 0.46 0.48 0.31
GTF2H2 ENST00000330280 85.58 75.76 83.96 0.28 0.43 0.35 0.46 0.88 0.43
CD1E ENST00000368167 85.59 86.23 89.03 0.28 0.27 0.19 0.46 0.43 0.26
LY6G6E ENST00000383418 85.59 96.07 93.59 0.28 0.21 0.13 0.46 0.20 0.15
C1orf227 ENST00000332912 85.60 80.49 86.27 0.28 0.37 0.33 0.46 0.58 0.33
ODF3L2 ENST00000315489 85.61 75.83 83.99 0.28 0.43 0.35 0.46 0.88 0.42
LYZL2 ENST00000375318 85.61 87.23 89.55 0.28 0.20 0.18 0.46 0.41 0.23

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