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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
ATP2A1 ENST00000357084 36.55 45.27 39.29 0.95 0.70 0.80 1.78 1.97 2.04
KIAA1161 ENST00000297625 36.55 73.98 54.84 0.95 0.53 0.53 1.78 1.02 1.74
RAB15 ENST00000267512 36.56 43.79 38.46 0.95 0.61 0.84 1.78 1.96 2.04
PTPRG ENST00000474889 36.56 21.17 27.04 0.95 1.46 0.99 1.78 0.81 1.29
DNAH2 ENST00000572933 36.57 28.93 30.97 0.95 1.15 0.82 1.78 1.30 1.51
CCM2L ENST00000262659 36.57 61.47 47.88 0.95 0.54 0.66 1.78 1.40 1.90
SOCS5 ENST00000306503 36.58 22.35 27.61 0.95 1.51 0.96 1.77 0.82 1.26
NAGLU ENST00000225927 36.58 48.63 40.78 0.95 0.63 0.81 1.77 2.00 2.04
SEPHS2 ENST00000500504 36.59 53.38 43.35 0.95 0.65 0.63 1.77 1.70 2.01
CIAO1 ENST00000488633 36.59 40.96 37.02 0.95 0.61 0.78 1.77 1.80 1.94
EHD4 ENST00000220325 36.60 44.36 38.77 0.95 0.62 0.82 1.78 1.95 2.03
CCDC127 ENST00000296824 36.60 63.85 49.14 0.95 0.49 0.72 1.77 1.20 1.83
APPL1 ENST00000288266 36.61 15.42 24.05 0.95 1.89 1.10 1.77 0.67 1.06
TMEM194A ENST00000300128 36.61 16.94 24.81 0.95 1.66 1.04 1.76 0.72 1.10
PLLP ENST00000219207 36.62 69.32 52.20 0.95 0.56 0.61 1.76 1.14 1.89
SLC6A7 ENST00000230671 36.63 52.61 42.96 0.95 0.68 0.67 1.77 1.80 2.00
SLC19A2 ENST00000236137 36.63 39.30 36.06 0.95 0.70 0.87 1.77 1.65 1.79
ULK3 ENST00000440863 36.64 25.47 29.20 0.95 1.25 0.84 1.76 1.06 1.33
HSD11B1 ENST00000367028 36.64 35.32 34.22 0.95 0.77 0.86 1.76 1.58 1.77
TFEB ENST00000230323 36.65 17.49 25.13 0.95 1.58 1.05 1.76 0.74 1.16
HNRNPUL2 ENST00000301785 36.65 8.04 20.43 0.95 2.53 1.51 1.76 0.44 0.88
CMTM8 ENST00000307526 36.66 54.37 43.91 0.95 0.61 0.61 1.76 1.68 2.02
ZNF329 ENST00000598312 36.66 48.86 40.98 0.95 0.63 0.76 1.76 2.03 2.05
CNR2 ENST00000536471 36.67 85.46 61.80 0.95 0.25 0.47 1.76 0.45 1.46
LAMP5 ENST00000246070 36.67 83.21 60.42 0.95 0.28 0.44 1.76 0.47 1.58

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