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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
hsa-mir-1199 ENST00000269720 91.68 71.25 85.06 0.14 0.53 0.33 0.20 1.07 0.38
PRRT4 ENST00000446477 91.69 42.90 69.72 0.14 0.62 0.44 0.20 1.92 0.94
EXOSC6 ENST00000435634 91.69 74.68 86.60 0.14 0.54 0.30 0.20 0.96 0.33
RP11-122A3.2 ENST00000517562 91.70 30.51 63.16 0.14 1.09 0.49 0.20 1.37 1.37
CCDC160 ENST00000517294 91.70 82.45 90.35 0.14 0.34 0.15 0.20 0.52 0.21
GAGE2A ENST00000362097 91.71 86.93 92.23 0.14 0.22 0.14 0.20 0.40 0.16
ZNF579 ENST00000325421 91.72 23.68 57.97 0.14 1.39 0.47 0.20 0.93 1.68
SMIM10 ENST00000330288 91.72 91.95 94.78 0.14 0.23 0.09 0.20 0.33 0.11
C16orf95 ENST00000567970 91.73 86.21 91.13 0.14 0.27 0.15 0.20 0.42 0.19
UTY ENST00000331397 91.73 13.59 51.56 0.14 2.05 0.62 0.20 0.59 1.93
AP000721.4 ENST00000535431 91.74 73.47 85.69 0.14 0.53 0.33 0.20 1.03 0.34
RP11-195F19.5 ENST00000421828 91.74 82.03 89.77 0.14 0.34 0.18 0.20 0.50 0.23
NPIPB4 ENST00000415645 91.75 47.77 72.19 0.14 0.59 0.43 0.20 1.99 0.81
AC090186.1 ENST00000415643 91.75 98.59 98.00 0.14 0.20 0.09 0.20 0.15 0.05
MTRNR2L8 ENST00000536684 91.76 98.60 97.99 0.14 0.20 0.09 0.20 0.15 0.04
POTED ENST00000299443 91.76 90.89 94.29 0.14 0.25 0.10 0.20 0.35 0.12
DEFB106B ENST00000335479 91.77 94.62 95.59 0.14 0.23 0.08 0.20 0.24 0.11
RP11-45H22.3 ENST00000505950 91.77 91.50 94.57 0.14 0.23 0.09 0.20 0.32 0.11
NPIPA7 ENST00000530217 91.78 96.35 97.04 0.14 0.22 0.08 0.20 0.19 0.07
NAT14 ENST00000205194 91.78 84.87 90.98 0.14 0.27 0.15 0.20 0.43 0.20
ZNF705B ENST00000443676 91.79 91.68 95.68 0.14 0.24 0.07 0.20 0.32 0.11
CDR2L ENST00000337231 91.79 40.80 68.51 0.14 0.62 0.47 0.20 1.78 1.06
NANOS1 ENST00000425699 91.80 70.73 85.26 0.14 0.48 0.34 0.20 1.08 0.36
KB-1507C5.2 ENST00000522939 91.80 89.58 93.33 0.14 0.27 0.13 0.20 0.37 0.15
AL590822.2 ENST00000597060 91.81 98.62 98.01 0.14 0.20 0.09 0.20 0.15 0.05

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