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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
C17orf78 ENST00000300618 45.20 80.40 64.08 0.63 0.37 0.52 1.75 0.59 1.37
LRRC10 ENST00000361484 45.20 49.40 46.02 0.63 0.65 0.68 1.75 2.01 1.96
IL17D ENST00000304920 45.21 81.75 64.89 0.63 0.33 0.51 1.75 0.52 1.33
FRK ENST00000606080 45.21 59.97 51.76 0.63 0.53 0.62 1.75 1.37 1.93
NSL1 ENST00000366977 45.22 47.83 45.20 0.63 0.59 0.70 1.75 1.98 2.00
MLH1 ENST00000231790 45.22 28.74 35.15 0.63 1.15 0.86 1.74 1.29 1.76
PMM1 ENST00000216259 45.23 65.52 54.96 0.63 0.53 0.51 1.74 1.23 1.74
DGKG ENST00000265022 45.24 44.86 43.41 0.63 0.68 0.63 1.74 1.99 2.01
TFEC ENST00000265440 45.24 62.01 53.02 0.63 0.56 0.61 1.74 1.36 1.87
CMTR2 ENST00000338099 45.25 61.09 52.45 0.63 0.53 0.61 1.75 1.39 1.92
NDRG4 ENST00000394282 45.25 29.16 35.41 0.63 1.13 0.87 1.75 1.34 1.77
HABP4 ENST00000375249 45.26 36.93 39.44 0.63 0.75 0.77 1.75 1.70 2.04
GPR37L1 ENST00000367282 45.26 77.43 62.13 0.63 0.42 0.48 1.75 0.76 1.44
PGPEP1 ENST00000269919 45.27 51.64 47.21 0.63 0.62 0.67 1.75 1.87 1.89
TECRL ENST00000381210 45.27 73.06 59.41 0.63 0.52 0.49 1.75 1.02 1.71
PPIL2 ENST00000412327 45.28 28.73 35.17 0.63 1.15 0.86 1.75 1.29 1.75
PMEL ENST00000449260 45.28 71.63 58.54 0.63 0.53 0.51 1.76 1.07 1.64
TATDN1 ENST00000276692 45.29 80.08 63.96 0.63 0.37 0.51 1.76 0.60 1.39
PALMD ENST00000263174 45.29 37.37 39.71 0.62 0.76 0.78 1.76 1.66 2.03
IGSF1 ENST00000370903 45.30 7.11 24.22 0.62 2.58 1.13 1.77 0.37 1.05
ZSWIM7 ENST00000399277 45.30 66.60 55.63 0.62 0.54 0.53 1.77 1.22 1.73
BSPRY ENST00000374183 45.31 67.71 56.27 0.62 0.52 0.49 1.76 1.19 1.75
DYNLT1 ENST00000367089 45.31 73.97 60.07 0.62 0.53 0.47 1.76 1.02 1.61
ZNF260 ENST00000523638 45.32 66.44 55.55 0.62 0.56 0.52 1.77 1.20 1.74
DUOX1 ENST00000321429 45.32 50.11 46.39 0.62 0.67 0.67 1.76 1.98 1.90

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