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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
CAMP ENST00000296435 86.00 74.79 83.79 0.25 0.53 0.34 0.44 0.95 0.41
HIST1H1A ENST00000244573 86.01 97.42 94.45 0.25 0.22 0.10 0.44 0.19 0.12
GHRH ENST00000373614 86.01 60.01 76.01 0.25 0.53 0.38 0.44 1.37 0.62
TPSD1 ENST00000211076 86.02 91.05 91.44 0.25 0.25 0.15 0.44 0.36 0.18
SLC35E2 ENST00000246421 86.02 85.39 88.82 0.25 0.25 0.19 0.44 0.45 0.28
TSPAN19 ENST00000532498 86.03 90.55 91.22 0.25 0.25 0.15 0.44 0.37 0.18
KIAA0125 ENST00000429431 86.03 86.53 89.40 0.25 0.24 0.18 0.44 0.42 0.24
FRG2B ENST00000425520 86.04 82.73 87.52 0.25 0.33 0.28 0.44 0.50 0.30
SNAPC2 ENST00000221573 86.04 47.40 68.74 0.25 0.66 0.46 0.44 2.01 1.05
C3orf52 ENST00000431717 86.05 89.73 90.93 0.25 0.27 0.15 0.43 0.37 0.20
MROH6 ENST00000398882 86.05 71.78 82.28 0.25 0.51 0.34 0.43 1.07 0.45
IFNGR1 ENST00000367739 86.06 35.51 61.48 0.25 0.77 0.44 0.43 1.57 1.47
C10orf99 ENST00000372126 86.06 82.73 87.54 0.25 0.33 0.28 0.43 0.50 0.30
WFDC10A ENST00000372643 86.07 95.89 93.78 0.25 0.22 0.10 0.43 0.20 0.13
UMODL1 ENST00000408989 86.08 62.41 77.44 0.25 0.52 0.35 0.43 1.32 0.58
TMPRSS11B ENST00000332644 86.08 85.77 89.04 0.25 0.27 0.19 0.43 0.44 0.26
C12orf71 ENST00000429849 86.09 86.29 89.29 0.25 0.25 0.19 0.43 0.43 0.25
ELANE ENST00000590230 86.09 61.10 76.69 0.25 0.53 0.34 0.43 1.39 0.60
MTERFD2 ENST00000391980 86.10 63.59 78.04 0.25 0.51 0.39 0.42 1.24 0.54
CES3 ENST00000303334 86.10 65.18 78.93 0.25 0.51 0.39 0.42 1.24 0.52
KRTAP10-9 ENST00000397911 86.11 88.41 90.30 0.25 0.23 0.15 0.42 0.37 0.21
CYP2A7 ENST00000301146 86.11 80.93 86.71 0.25 0.35 0.30 0.42 0.57 0.32
ALPPL2 ENST00000295453 86.12 78.07 85.45 0.25 0.43 0.33 0.42 0.74 0.35
AADACL3 ENST00000359318 86.12 85.42 88.91 0.25 0.25 0.19 0.42 0.45 0.28
ALPK2 ENST00000361673 86.13 42.89 66.19 0.25 0.62 0.52 0.42 1.91 1.20

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