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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
RCOR2 ENST00000301459 28.41 23.01 23.75 1.18 1.44 1.14 1.51 0.91 1.02
PTAR1 ENST00000340434 28.42 18.68 21.65 1.18 1.52 1.27 1.51 0.75 0.91
SLC4A3 ENST00000373762 28.42 28.10 26.36 1.18 1.19 1.00 1.51 1.20 1.26
EML5 ENST00000554922 28.43 17.23 20.94 1.18 1.61 1.43 1.51 0.74 0.88
SLIT1 ENST00000266058 28.43 6.47 15.22 1.18 2.62 1.83 1.51 0.37 0.64
GMPR2 ENST00000420554 28.44 68.68 47.31 1.18 0.53 0.66 1.51 1.18 1.87
KIAA1841 ENST00000402291 28.44 34.45 29.63 1.18 0.80 0.85 1.51 1.56 1.40
PALM2 ENST00000314527 28.45 38.71 31.81 1.18 0.70 0.89 1.51 1.67 1.58
DHX36 ENST00000496811 28.45 14.65 19.57 1.18 2.00 1.53 1.52 0.61 0.85
MIER1 ENST00000401041 28.46 18.45 21.63 1.18 1.48 1.27 1.52 0.76 0.92
AIP ENST00000279146 28.46 26.02 25.34 1.18 1.20 1.05 1.52 1.10 1.17
ST8SIA2 ENST00000268164 28.47 33.06 28.90 1.16 0.85 0.81 1.53 1.49 1.31
TMEM66 ENST00000256255 28.47 44.24 34.57 1.15 0.62 0.90 1.53 1.95 1.77
LRRN1 ENST00000319331 28.48 13.54 19.01 1.16 2.06 1.54 1.53 0.61 0.85
GJC2 ENST00000366714 28.49 68.18 47.07 1.16 0.52 0.68 1.53 1.22 1.88
EMC6 ENST00000397133 28.49 69.81 48.00 1.16 0.54 0.67 1.53 1.14 1.87
ARHGEF6 ENST00000250617 28.50 2.28 12.94 1.16 3.64 2.10 1.53 0.29 0.53
SYT17 ENST00000355377 28.50 50.12 37.59 1.16 0.67 0.84 1.53 1.99 2.01
ITSN2 ENST00000355123 28.51 22.99 23.82 1.16 1.46 1.10 1.53 0.91 1.04
GFRA1 ENST00000355422 28.51 26.20 25.42 1.16 1.19 1.04 1.53 1.08 1.17
ABCB1 ENST00000265724 28.52 23.38 24.00 1.16 1.40 1.10 1.53 0.93 1.05
VPS41 ENST00000310301 28.52 44.29 34.64 1.16 0.61 0.90 1.53 1.95 1.76
DCAF17 ENST00000375255 28.53 39.76 32.33 1.16 0.65 0.90 1.53 1.66 1.61
CEP85L ENST00000368488 28.53 37.01 30.98 1.16 0.77 0.82 1.53 1.68 1.51
CCNB1IP1 ENST00000398169 28.54 60.54 42.86 1.16 0.52 0.68 1.53 1.41 2.01

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