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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
NACA ENST00000550952 12.01 37.69 23.02 1.66 0.78 1.20 0.61 1.70 0.98
LRRC4 ENST00000249363 12.02 4.04 5.31 1.66 3.25 3.56 0.61 0.32 0.25
RICTOR ENST00000357387 12.02 3.18 4.85 1.66 3.47 3.68 0.61 0.28 0.24
AGAP3 ENST00000397238 12.03 15.25 11.31 1.66 1.90 2.18 0.61 0.67 0.45
IRF2 ENST00000393593 12.03 19.68 13.47 1.66 1.42 2.06 0.61 0.74 0.57
KCTD1 ENST00000408011 12.04 21.35 14.43 1.66 1.43 2.00 0.61 0.80 0.59
FAXC ENST00000389677 12.04 18.13 12.65 1.66 1.53 2.19 0.61 0.74 0.52
DYNC1LI2 ENST00000258198 12.05 12.25 9.61 1.66 2.06 2.26 0.61 0.58 0.40
INSIG2 ENST00000245787 12.06 40.12 24.09 1.64 0.63 1.10 0.61 1.71 1.06
CDH10 ENST00000264463 12.06 19.48 13.38 1.64 1.44 2.05 0.61 0.74 0.55
YKT6 ENST00000223369 12.07 30.10 19.07 1.66 1.08 1.54 0.61 1.41 0.85
INF2 ENST00000392634 12.07 11.20 9.01 1.66 2.10 2.44 0.61 0.54 0.38
TBP ENST00000392092 12.08 28.99 18.46 1.66 1.15 1.62 0.61 1.31 0.81
RNF220 ENST00000355387 12.08 6.82 6.79 1.67 2.63 2.97 0.61 0.37 0.32
UBAC2 ENST00000403766 12.09 38.74 23.51 1.67 0.70 1.18 0.61 1.67 1.01
SLC12A6 ENST00000354181 12.09 18.42 12.79 1.67 1.47 2.11 0.61 0.75 0.52
SP4 ENST00000222584 12.10 10.82 8.84 1.67 2.13 2.48 0.61 0.50 0.38
STK39 ENST00000355999 12.10 7.63 7.23 1.67 2.49 2.81 0.61 0.42 0.34
GPR12 ENST00000405846 12.11 36.19 22.31 1.67 0.82 1.16 0.61 1.61 0.96
HTR4 ENST00000360693 12.11 33.82 21.12 1.67 0.85 1.42 0.61 1.56 0.90
SEC63 ENST00000369002 12.12 25.95 16.87 1.67 1.20 1.68 0.61 1.10 0.70
TMEM161B ENST00000296595 12.12 35.11 21.74 1.67 0.76 1.25 0.61 1.58 0.93
EI24 ENST00000278903 12.13 20.60 14.04 1.67 1.44 2.04 0.61 0.76 0.60
SPRED1 ENST00000299084 12.13 14.66 11.05 1.67 2.00 2.20 0.61 0.62 0.44
ZC3H10 ENST00000257940 12.14 30.35 19.26 1.67 1.08 1.54 0.61 1.40 0.85

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