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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
ARPP19 ENST00000566423 15.24 31.38 21.44 1.57 0.96 1.32 0.75 1.41 0.91
CUL4A ENST00000375440 15.25 1.98 5.86 1.57 3.74 3.29 0.75 0.27 0.29
GOLT1B ENST00000229314 15.25 23.89 17.44 1.57 1.39 1.62 0.75 0.95 0.76
MOV10 ENST00000413052 15.26 16.36 13.42 1.57 1.80 2.05 0.75 0.69 0.55
B3GALT1 ENST00000392690 15.26 45.79 28.68 1.57 0.75 0.80 0.75 2.01 1.34
IL1RAPL2 ENST00000372582 15.27 11.83 11.23 1.57 2.09 2.15 0.75 0.58 0.45
ZBTB38 ENST00000514251 15.27 7.51 8.74 1.57 2.52 2.49 0.75 0.40 0.37
RAB5A ENST00000273047 15.28 30.13 20.86 1.57 1.09 1.47 0.75 1.41 0.87
NCALD ENST00000395923 15.28 19.16 15.03 1.57 1.49 1.89 0.75 0.76 0.63
MYCN ENST00000281043 15.29 19.10 15.00 1.57 1.51 1.89 0.75 0.76 0.63
TRIM23 ENST00000231524 15.29 29.45 20.48 1.56 1.09 1.49 0.75 1.38 0.89
CTNNBL1 ENST00000361383 15.30 26.72 19.01 1.56 1.20 1.54 0.75 1.11 0.85
SREK1 ENST00000334121 15.30 12.85 11.72 1.56 2.07 2.21 0.75 0.59 0.47
ABHD2 ENST00000352732 15.31 20.21 15.59 1.56 1.43 1.77 0.75 0.74 0.66
SH2D1A ENST00000371139 15.31 51.77 31.77 1.56 0.61 0.89 0.75 1.89 1.58
ANKS1A ENST00000360359 15.32 15.44 12.92 1.56 1.89 2.10 0.75 0.67 0.53
SCRT2 ENST00000246104 15.32 17.71 14.22 1.56 1.53 1.99 0.76 0.73 0.59
UBA6 ENST00000322244 15.33 26.92 19.12 1.56 1.23 1.53 0.76 1.12 0.85
TNNI3 ENST00000344887 15.33 37.44 24.43 1.56 0.76 1.08 0.76 1.66 1.08
LRP6 ENST00000261349 15.34 11.77 11.23 1.56 2.09 2.15 0.76 0.57 0.45
USP37 ENST00000258399 15.35 5.25 7.64 1.56 3.14 2.72 0.76 0.32 0.33
MAPK8IP3 ENST00000250894 15.35 2.95 6.51 1.56 3.49 3.05 0.76 0.29 0.32
FBXO42 ENST00000375592 15.36 11.28 10.95 1.56 2.13 2.23 0.76 0.55 0.44
NKTR ENST00000232978 15.36 11.03 10.79 1.56 2.10 2.19 0.76 0.52 0.43
FBXO18 ENST00000379999 15.37 20.18 15.58 1.56 1.43 1.77 0.76 0.75 0.66

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