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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
MAGEA1 ENST00000356661 98.14 98.44 99.66 0.11 0.21 0.12 0.11 0.14 0.04
C3orf36 ENST00000408895 98.15 99.45 99.84 0.11 0.16 0.12 0.11 0.12 0.04
TP53AIP1 ENST00000531399 98.15 96.55 99.15 0.11 0.22 0.11 0.11 0.19 0.04
PRAMEF1 ENST00000332296 98.16 94.61 98.56 0.11 0.23 0.10 0.11 0.24 0.05
SPATA32 ENST00000331780 98.16 79.70 91.75 0.11 0.37 0.15 0.11 0.64 0.18
CD1C ENST00000368170 98.17 67.46 86.05 0.11 0.54 0.33 0.11 1.20 0.33
FAM186A ENST00000327337 98.17 41.93 72.76 0.11 0.61 0.43 0.11 1.83 0.81
ZNF221 ENST00000251269 98.18 83.73 93.75 0.11 0.27 0.10 0.11 0.47 0.13
ZNF530 ENST00000332854 98.18 90.08 96.91 0.11 0.25 0.08 0.11 0.37 0.07
ZIK1 ENST00000597850 98.19 93.48 98.20 0.11 0.28 0.09 0.11 0.28 0.05
PRR23A ENST00000383163 98.19 99.96 99.90 0.11 0.18 0.12 0.11 0.09 0.04
LCN9 ENST00000277526 98.20 49.87 77.21 0.11 0.66 0.35 0.11 2.02 0.59
KLK3 ENST00000326003 98.20 77.80 90.98 0.11 0.42 0.15 0.11 0.79 0.20
CXorf48 ENST00000276241 98.21 43.18 73.49 0.11 0.62 0.40 0.11 1.91 0.76
C11orf24 ENST00000304271 98.21 87.71 95.74 0.11 0.24 0.07 0.11 0.37 0.11
C10orf129 ENST00000341686 98.22 55.35 80.12 0.11 0.57 0.35 0.11 1.61 0.53
C19orf57 ENST00000346736 98.22 41.71 72.66 0.11 0.61 0.43 0.11 1.80 0.81
PRB4 ENST00000279575 98.23 97.43 99.39 0.09 0.22 0.11 0.11 0.19 0.04
TCEB3CL2 ENST00000591973 98.23 98.83 99.73 0.09 0.16 0.12 0.11 0.14 0.04
MNDA ENST00000368141 98.24 91.02 97.30 0.09 0.25 0.08 0.11 0.35 0.07
HRNR ENST00000368801 98.24 96.50 99.17 0.09 0.22 0.11 0.11 0.19 0.04
SPACA7 ENST00000283550 98.25 71.28 87.88 0.09 0.53 0.24 0.11 1.07 0.32
FAM90A1 ENST00000538603 98.25 94.17 98.46 0.09 0.25 0.10 0.10 0.25 0.05
GTSE1 ENST00000454366 98.26 37.35 70.03 0.09 0.76 0.47 0.10 1.65 0.91
OR7G1 ENST00000541538 98.26 99.88 99.87 0.09 0.17 0.12 0.10 0.11 0.04

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