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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
RTN3 ENST00000377819 37.19 33.83 33.69 0.94 0.85 0.90 1.73 1.56 1.73
NPAT ENST00000278612 37.20 14.92 24.07 0.94 1.94 1.10 1.73 0.63 1.06
CNST ENST00000366513 37.20 38.39 35.92 0.94 0.75 0.86 1.73 1.71 1.79
TMTC2 ENST00000321196 37.21 23.17 28.38 0.94 1.46 0.80 1.73 0.90 1.29
SERP1 ENST00000479209 37.21 69.27 52.55 0.95 0.57 0.61 1.73 1.14 1.90
NUP188 ENST00000372577 37.22 12.13 22.81 0.95 2.07 1.19 1.73 0.57 0.98
HS3ST4 ENST00000331351 37.22 25.47 29.53 0.95 1.25 0.84 1.73 1.06 1.37
ASPA ENST00000263080 37.23 60.48 47.66 0.95 0.52 0.65 1.73 1.41 1.88
LRIG3 ENST00000320743 37.23 31.67 32.65 0.95 0.94 0.86 1.73 1.45 1.63
SLC6A5 ENST00000525748 37.24 52.69 43.31 0.95 0.67 0.63 1.73 1.80 2.01
FAM179B ENST00000361577 37.24 26.30 29.97 0.95 1.19 0.85 1.73 1.08 1.46
MRPL43 ENST00000342071 37.25 77.57 57.31 0.95 0.42 0.51 1.73 0.79 1.68
GPR26 ENST00000284674 37.26 30.21 31.94 0.95 1.09 0.91 1.72 1.41 1.57
CEP97 ENST00000341893 37.26 42.96 38.40 0.95 0.63 0.84 1.72 1.90 2.04
LZTS1 ENST00000381569 37.27 15.29 24.34 0.95 1.90 1.09 1.72 0.67 1.07
CMTM4 ENST00000330687 37.27 47.22 40.49 0.95 0.66 0.80 1.72 2.00 2.04
SHROOM3 ENST00000296043 37.28 15.60 24.49 0.95 1.86 1.08 1.72 0.68 1.08
PSENEN ENST00000587708 37.28 26.37 29.99 0.95 1.18 0.85 1.72 1.08 1.46
CYBRD1 ENST00000321348 37.29 47.84 40.74 0.95 0.59 0.81 1.72 1.98 2.05
ERCC8 ENST00000265038 37.29 72.93 54.70 0.95 0.51 0.57 1.72 1.02 1.73
CEP85 ENST00000252992 37.30 25.01 29.33 0.95 1.33 0.82 1.72 1.05 1.34
ACO1 ENST00000309951 37.30 50.41 42.09 0.95 0.66 0.71 1.72 1.95 1.99
ADAMTS4 ENST00000367996 37.31 36.68 35.16 0.95 0.78 0.86 1.72 1.66 1.75
FAP ENST00000188790 37.31 57.24 45.96 0.95 0.56 0.70 1.72 1.49 1.97
ZNF18 ENST00000322748 37.32 39.89 36.78 0.95 0.63 0.82 1.72 1.70 1.94

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