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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
CEP68 ENST00000377990 71.41 21.44 45.10 0.37 1.43 0.70 0.83 0.80 2.02
OR5B3 ENST00000309403 71.42 92.33 85.22 0.37 0.25 0.34 0.83 0.30 0.37
ZNF140 ENST00000355557 71.42 89.39 83.79 0.37 0.27 0.34 0.83 0.37 0.41
PLEKHG2 ENST00000409794 71.43 31.60 50.54 0.37 0.94 0.67 0.83 1.44 1.86
CTRC ENST00000375949 71.43 88.34 83.25 0.37 0.23 0.29 0.83 0.37 0.40
RDM1 ENST00000293273 71.44 83.12 80.60 0.37 0.29 0.39 0.83 0.49 0.52
ZFP69B ENST00000411995 71.44 77.86 77.85 0.37 0.42 0.38 0.83 0.79 0.54
PLAC1L ENST00000278855 71.45 71.86 74.58 0.37 0.51 0.40 0.83 1.07 0.68
AMICA1 ENST00000356289 71.45 44.46 58.02 0.37 0.63 0.47 0.83 1.98 1.66
ZNF391 ENST00000244576 71.46 78.88 78.41 0.37 0.40 0.38 0.83 0.70 0.54
C1orf54 ENST00000369102 71.46 81.99 80.05 0.37 0.35 0.35 0.83 0.50 0.52
ALS2CL ENST00000318962 71.47 60.55 67.91 0.37 0.52 0.51 0.83 1.41 1.10
OR5B12 ENST00000302572 71.47 77.66 77.76 0.37 0.42 0.38 0.83 0.79 0.55
GRP ENST00000256857 71.48 88.56 83.38 0.37 0.24 0.33 0.83 0.36 0.40
PTK6 ENST00000217185 71.48 73.44 75.38 0.37 0.53 0.37 0.83 1.03 0.65
PHPT1 ENST00000247665 71.49 90.23 84.14 0.37 0.25 0.34 0.83 0.38 0.42
PNPLA7 ENST00000406427 71.49 58.59 66.76 0.37 0.54 0.53 0.83 1.42 1.20
LRRIQ1 ENST00000393217 71.50 50.76 61.89 0.37 0.63 0.48 0.83 1.95 1.44
ZNHIT3 ENST00000225410 71.50 89.88 83.97 0.37 0.27 0.35 0.83 0.37 0.43
SEMA3G ENST00000231721 71.51 59.78 67.44 0.37 0.52 0.52 0.83 1.37 1.14
ZWINT ENST00000373944 71.51 73.35 75.34 0.35 0.54 0.37 0.83 1.02 0.65
OR5K1 ENST00000332650 71.52 95.64 86.75 0.35 0.23 0.30 0.83 0.21 0.32
DCST2 ENST00000368424 71.53 48.07 60.24 0.37 0.63 0.47 0.83 1.99 1.60
TIMM13 ENST00000215570 71.53 81.47 79.82 0.37 0.33 0.38 0.83 0.54 0.52
DCAF12L2 ENST00000538699 71.54 60.24 67.78 0.37 0.53 0.52 0.82 1.38 1.12

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