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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
RP11-487E13.1 ENST00000512516 93.75 78.01 87.70 0.11 0.42 0.24 0.13 0.77 0.31
NKPD1 ENST00000317951 93.76 44.05 71.48 0.11 0.61 0.46 0.13 1.97 0.86
ANHX ENST00000545940 93.76 29.86 62.83 0.11 1.13 0.49 0.13 1.40 1.40
GAGE2C ENST00000381708 93.77 90.29 94.82 0.11 0.25 0.09 0.13 0.38 0.11
CPSF4L ENST00000344935 93.77 57.77 79.14 0.11 0.57 0.39 0.13 1.47 0.54
TMEM151B ENST00000451188 93.78 28.97 61.00 0.11 1.15 0.43 0.13 1.31 1.57
SPINT3 ENST00000217428 93.78 95.65 96.70 0.11 0.23 0.08 0.13 0.20 0.08
DSCR8 ENST00000357704 93.79 97.00 97.92 0.11 0.24 0.09 0.13 0.19 0.04
C1orf134 ENST00000375605 93.79 93.77 95.20 0.11 0.27 0.08 0.13 0.26 0.10
UTF1 ENST00000304477 93.80 76.73 88.44 0.11 0.40 0.22 0.13 0.83 0.29
PFN3 ENST00000358571 93.80 74.73 86.63 0.11 0.54 0.30 0.13 0.96 0.33
RP11-321F6.1 ENST00000558797 93.81 84.77 90.66 0.11 0.27 0.15 0.13 0.42 0.20
RP11-497E19.2 ENST00000553678 93.81 87.65 93.50 0.11 0.24 0.11 0.13 0.36 0.15
RP11-322L20.1 ENST00000557527 93.82 85.65 92.48 0.11 0.27 0.14 0.13 0.44 0.15
VWA5B2 ENST00000426955 93.82 31.03 62.49 0.11 1.04 0.48 0.13 1.36 1.40
TBL1Y ENST00000383032 93.83 97.29 97.39 0.11 0.23 0.08 0.13 0.19 0.07
AC002472.13 ENST00000342608 93.83 84.41 91.80 0.11 0.29 0.14 0.13 0.44 0.18
GOLGA6L6 ENST00000427390 93.84 79.17 88.85 0.11 0.39 0.19 0.13 0.69 0.28
SPATA31A2 ENST00000456183 93.84 87.68 93.58 0.11 0.24 0.13 0.13 0.36 0.15
TMEM235 ENST00000551068 93.85 77.68 88.61 0.11 0.42 0.22 0.13 0.79 0.28
PRAMEF15 ENST00000330087 93.85 92.01 95.84 0.11 0.24 0.07 0.13 0.33 0.11
DEFB105A ENST00000334773 93.86 88.35 93.13 0.11 0.23 0.14 0.13 0.37 0.15
PLK5 ENST00000334770 93.86 65.60 83.15 0.11 0.53 0.29 0.13 1.22 0.40
BSPH1 ENST00000344839 93.87 62.26 81.45 0.11 0.53 0.35 0.13 1.33 0.48
AL360004.1 ENST00000358748 93.87 99.75 97.76 0.11 0.17 0.09 0.13 0.11 0.04

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