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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
IFNA5 ENST00000259555 97.84 99.48 99.78 0.11 0.16 0.12 0.11 0.13 0.04
MBD3L1 ENST00000595891 80.24 99.48 92.10 0.32 0.16 0.14 0.58 0.13 0.16
ZNF497 ENST00000311044 94.83 99.49 99.09 0.10 0.16 0.11 0.11 0.13 0.04
BLID ENST00000560104 96.18 99.49 99.43 0.11 0.16 0.11 0.11 0.13 0.05
C10orf111 ENST00000378207 98.82 99.50 99.93 0.10 0.16 0.12 0.11 0.13 0.04
SPRR2A ENST00000392653 84.40 99.50 94.73 0.30 0.16 0.09 0.46 0.13 0.11
PRR21 ENST00000408934 89.40 99.51 96.50 0.16 0.16 0.07 0.32 0.13 0.07
HEPN1 ENST00000408930 87.35 99.51 96.20 0.23 0.16 0.07 0.38 0.13 0.10
TAS2R16 ENST00000249284 88.84 99.52 96.98 0.19 0.16 0.08 0.32 0.13 0.07
OR7E24 ENST00000456448 96.81 99.52 99.11 0.09 0.16 0.11 0.11 0.13 0.04
AP001885.1 ENST00000444002 93.36 99.53 96.72 0.15 0.16 0.08 0.15 0.13 0.08
AC074389.6 ENST00000382528 97.95 99.54 99.80 0.11 0.16 0.12 0.11 0.13 0.04
SRY ENST00000383070 93.37 99.54 97.44 0.15 0.16 0.08 0.15 0.13 0.07
AC008132.13 ENST00000342005 93.39 99.55 97.57 0.13 0.16 0.09 0.15 0.13 0.06
TAS2R10 ENST00000240619 88.56 99.55 96.89 0.20 0.16 0.08 0.34 0.13 0.07
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
IVL ENST00000368764 98.48 99.18 99.85 0.10 0.15 0.12 0.11 0.13 0.04
MRGPRG ENST00000332314 92.74 99.19 98.20 0.15 0.15 0.09 0.17 0.13 0.05
KRTAP21-3 ENST00000444335 92.76 99.19 97.98 0.15 0.15 0.09 0.17 0.13 0.04
TCEB3CL ENST00000451265 99.93 99.20 99.98 0.10 0.15 0.13 0.14 0.13 0.04
KRTAP19-3 ENST00000334063 88.82 99.20 96.89 0.19 0.15 0.08 0.33 0.13 0.07
FAM106A ENST00000392176 92.79 99.21 98.47 0.15 0.15 0.10 0.17 0.13 0.05
MRGPRX2 ENST00000329773 98.74 99.21 99.89 0.10 0.15 0.12 0.11 0.13 0.04
OR1N1 ENST00000304880 95.53 99.22 99.22 0.11 0.15 0.11 0.11 0.13 0.04
AL161915.1 ENST00000391366 92.80 99.23 98.14 0.15 0.15 0.09 0.17 0.13 0.05

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