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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
TBC1D9 ENST00000442267 17.95 24.23 19.08 1.53 1.32 1.54 0.89 0.98 0.85
PHC3 ENST00000495893 17.96 1.00 6.82 1.53 4.07 2.96 0.89 0.28 0.33
DNAJC3 ENST00000602402 17.96 27.50 20.87 1.53 1.25 1.47 0.89 1.16 0.87
STAM ENST00000377524 17.97 17.21 15.38 1.53 1.59 1.81 0.89 0.74 0.66
ZNF32 ENST00000395797 17.97 47.57 30.98 1.53 0.61 0.82 0.89 2.01 1.51
POMP ENST00000380842 17.98 17.87 15.73 1.53 1.52 1.77 0.89 0.72 0.66
POLR2C ENST00000219252 17.98 45.30 29.84 1.53 0.70 0.87 0.89 1.97 1.43
RALY ENST00000246194 17.99 37.76 26.04 1.53 0.80 0.99 0.89 1.70 1.25
ADAR ENST00000368474 17.99 19.36 16.50 1.53 1.49 1.71 0.89 0.75 0.69
WDR45 ENST00000356463 18.00 7.10 10.10 1.52 2.57 2.24 0.89 0.37 0.43
PCDH17 ENST00000377918 18.01 15.77 14.63 1.52 1.89 1.97 0.89 0.69 0.59
GCM2 ENST00000379491 18.01 42.72 28.53 1.53 0.62 0.78 0.89 1.92 1.32
RNF31 ENST00000324103 18.02 5.20 8.99 1.53 3.16 2.45 0.89 0.32 0.38
SEC24C ENST00000339365 18.02 4.25 8.50 1.53 3.26 2.51 0.89 0.32 0.37
FAM169A ENST00000389156 18.03 5.12 8.95 1.53 3.20 2.48 0.89 0.33 0.38
PRPF40B ENST00000548825 18.03 8.91 11.12 1.53 2.44 2.19 0.89 0.47 0.45
VSX2 ENST00000261980 18.04 57.38 35.80 1.53 0.54 0.85 0.90 1.49 1.78
ATP8B2 ENST00000368489 18.04 20.84 17.32 1.53 1.42 1.63 0.89 0.83 0.75
HS6ST3 ENST00000376705 18.05 6.85 10.02 1.53 2.62 2.26 0.89 0.37 0.42
BEND5 ENST00000371833 18.05 30.11 22.24 1.53 1.08 1.15 0.90 1.41 0.96
SLC17A6 ENST00000263160 18.06 23.10 18.54 1.53 1.47 1.62 0.90 0.91 0.81
RP11-724O16.1 ENST00000513963 18.06 39.35 26.89 1.53 0.70 0.97 0.90 1.65 1.27
IL21 ENST00000264497 18.07 32.80 23.53 1.53 0.84 1.18 0.90 1.44 1.01
TTBK2 ENST00000267890 18.07 9.81 11.62 1.53 2.40 2.23 0.90 0.49 0.45
ARAF ENST00000377045 18.08 15.17 14.35 1.53 1.90 2.00 0.90 0.67 0.59

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