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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
TMEM63A ENST00000366835 48.04 43.73 44.35 0.54 0.62 0.61 1.80 1.95 2.04
TLCD1 ENST00000292090 48.05 59.58 53.25 0.54 0.52 0.61 1.80 1.41 1.88
PNO1 ENST00000263657 48.05 34.69 39.72 0.54 0.80 0.78 1.79 1.55 2.03
ACSM3 ENST00000289416 48.06 58.47 52.57 0.54 0.54 0.61 1.79 1.39 1.89
ZSCAN25 ENST00000394152 48.06 38.46 41.50 0.54 0.75 0.73 1.79 1.70 2.02
SLC35D2 ENST00000253270 48.07 83.43 67.56 0.54 0.27 0.51 1.78 0.47 1.13
CLRN2 ENST00000511148 48.07 81.86 66.68 0.54 0.35 0.53 1.78 0.51 1.20
CHFR ENST00000432561 48.08 27.24 35.76 0.54 1.25 0.85 1.78 1.15 1.78
COPG2 ENST00000445977 48.08 44.40 44.90 0.54 0.61 0.68 1.78 1.97 2.03
FAH ENST00000407106 48.09 75.18 62.50 0.54 0.49 0.48 1.78 0.91 1.40
AMT ENST00000273588 48.09 42.61 43.70 0.54 0.59 0.61 1.78 1.90 2.01
SP7 ENST00000536324 48.10 28.78 36.54 0.54 1.14 0.85 1.78 1.29 1.90
CTTN ENST00000376561 48.10 21.57 32.99 0.54 1.44 0.85 1.78 0.81 1.67
AFP ENST00000395792 48.11 49.44 47.56 0.54 0.65 0.65 1.78 2.01 1.89
SYT13 ENST00000020926 48.11 22.67 33.54 0.54 1.46 0.89 1.78 0.88 1.72
MTIF2 ENST00000394600 48.12 46.55 46.04 0.56 0.75 0.68 1.78 2.02 1.97
MORN5 ENST00000373764 48.12 79.18 65.11 0.56 0.39 0.51 1.78 0.69 1.31
RASSF9 ENST00000361228 48.13 67.25 57.65 0.56 0.56 0.51 1.78 1.21 1.67
S100Z ENST00000317593 48.13 87.67 70.13 0.56 0.24 0.46 1.78 0.36 0.90
UNC45A ENST00000418476 48.14 38.64 41.63 0.56 0.71 0.72 1.78 1.66 2.01
CGRRF1 ENST00000216420 48.14 43.16 44.07 0.56 0.62 0.61 1.78 1.90 2.03
KLHL36 ENST00000564996 48.15 18.41 31.49 0.56 1.47 0.86 1.78 0.75 1.57
ANKRD22 ENST00000371930 48.15 87.87 70.28 0.56 0.24 0.43 1.78 0.38 0.91
FAM213A ENST00000372181 48.16 86.46 69.48 0.56 0.24 0.44 1.78 0.42 0.98
ABCD4 ENST00000356924 48.16 49.57 47.70 0.56 0.66 0.65 1.78 2.03 1.89

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