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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
AC110615.1 ENST00000599764 59.40 91.09 78.49 0.57 0.25 0.38 1.44 0.35 0.54
FAXDC2 ENST00000326080 59.41 68.02 65.15 0.57 0.52 0.52 1.44 1.19 1.31
OR52I1 ENST00000530443 59.41 63.88 62.51 0.57 0.49 0.48 1.43 1.21 1.39
RASAL1 ENST00000546530 59.42 53.11 55.96 0.57 0.66 0.49 1.43 1.77 1.76
NMUR2 ENST00000255262 59.42 58.73 59.32 0.57 0.54 0.51 1.43 1.43 1.69
LCE1A ENST00000335123 59.43 95.03 80.55 0.57 0.23 0.39 1.44 0.21 0.51
C4orf22 ENST00000508675 59.43 85.44 75.36 0.57 0.25 0.37 1.43 0.45 0.66
GRM6 ENST00000231188 59.44 66.18 64.08 0.57 0.53 0.52 1.44 1.20 1.37
MPZL2 ENST00000278937 59.44 93.08 79.52 0.57 0.28 0.38 1.44 0.30 0.52
CDX2 ENST00000381020 59.45 30.26 43.22 0.57 1.09 0.65 1.43 1.40 1.99
ZNF283 ENST00000324461 59.45 58.40 59.08 0.57 0.54 0.49 1.43 1.41 1.68
PGAM2 ENST00000297283 59.46 87.12 76.39 0.57 0.22 0.37 1.43 0.41 0.61
ANKRD23 ENST00000318357 59.46 91.60 78.78 0.57 0.23 0.39 1.43 0.32 0.52
CCDC167 ENST00000373408 59.47 96.37 81.27 0.57 0.22 0.38 1.43 0.19 0.48
SHC4 ENST00000332408 59.48 51.13 54.86 0.57 0.66 0.52 1.43 1.91 1.74
COX20 ENST00000411948 59.48 80.39 72.62 0.57 0.37 0.46 1.43 0.59 0.81
SQRDL ENST00000260324 59.49 66.96 64.57 0.57 0.53 0.51 1.43 1.25 1.34
SPINT2 ENST00000301244 59.49 53.83 56.50 0.57 0.63 0.52 1.43 1.71 1.70
CELSR1 ENST00000262738 59.50 8.24 32.05 0.57 2.56 0.90 1.43 0.45 1.60
CCDC110 ENST00000307588 59.50 68.04 65.23 0.57 0.52 0.53 1.43 1.19 1.31
PEX26 ENST00000329627 59.51 16.06 35.90 0.57 1.82 0.86 1.43 0.68 1.79
LAPTM4B ENST00000445593 59.51 83.60 74.46 0.57 0.27 0.40 1.43 0.47 0.69
C1orf112 ENST00000286031 59.52 36.14 46.49 0.57 0.82 0.67 1.43 1.60 1.91
TMEM241 ENST00000383233 59.52 46.75 52.41 0.57 0.72 0.61 1.42 1.97 1.91
TEP1 ENST00000262715 59.53 45.22 51.52 0.57 0.70 0.62 1.41 1.98 1.92

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