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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
GLRA1 ENST00000455880 13.18 40.57 24.92 1.71 0.63 1.02 0.64 1.76 1.11
FOXC1 ENST00000380874 13.18 13.14 10.76 1.72 2.06 2.19 0.64 0.60 0.43
CBX8 ENST00000269385 13.19 9.26 8.55 1.71 2.47 2.51 0.64 0.46 0.37
B3GNT2 ENST00000301998 13.19 21.84 15.28 1.71 1.47 1.83 0.64 0.81 0.66
LUM ENST00000266718 13.20 50.83 30.20 1.70 0.63 0.81 0.64 1.92 1.44
SERTM1 ENST00000315190 13.20 75.17 42.45 1.70 0.49 0.68 0.64 0.91 2.01
UCHL5 ENST00000367455 13.21 32.97 21.18 1.70 0.84 1.40 0.64 1.49 0.90
SLC39A10 ENST00000409086 13.21 4.46 6.09 1.70 3.27 3.26 0.64 0.32 0.30
EDC4 ENST00000358933 13.22 17.42 12.85 1.70 1.59 2.11 0.64 0.73 0.53
TSSK6 ENST00000360913 13.22 29.84 19.54 1.70 1.13 1.54 0.64 1.40 0.84
PHF20 ENST00000374012 13.23 9.48 8.69 1.70 2.48 2.52 0.64 0.49 0.37
GRM3 ENST00000361669 13.23 17.04 12.67 1.70 1.62 2.18 0.65 0.73 0.52
SV2A ENST00000369146 13.24 21.14 15.01 1.70 1.47 1.89 0.65 0.81 0.63
SNX33 ENST00000308527 13.24 31.58 20.55 1.70 0.94 1.48 0.65 1.44 0.89
ZNF704 ENST00000327835 13.25 7.94 7.96 1.68 2.53 2.59 0.65 0.44 0.36
SLC8A1 ENST00000403092 13.25 10.28 9.24 1.67 2.28 2.32 0.65 0.49 0.38
EIF3M ENST00000531120 13.26 32.29 20.91 1.67 0.86 1.44 0.65 1.46 0.87
TBX20 ENST00000408931 13.26 12.93 10.70 1.67 2.06 2.18 0.65 0.59 0.43
PHTF2 ENST00000416283 13.27 24.98 16.98 1.67 1.33 1.67 0.65 1.05 0.70
DPYSL5 ENST00000288699 13.27 1.59 4.76 1.67 3.86 3.67 0.66 0.26 0.25
SOX21 ENST00000376945 13.28 38.86 24.08 1.67 0.70 1.10 0.66 1.66 1.06
PTPN4 ENST00000263708 13.28 9.73 8.88 1.67 2.43 2.48 0.66 0.50 0.38
PIP5K1C ENST00000335312 13.29 13.70 11.14 1.67 2.06 2.19 0.66 0.59 0.45
NR6A1 ENST00000487099 13.29 13.07 10.77 1.67 2.07 2.19 0.66 0.59 0.43
INIP ENST00000374242 13.30 67.11 38.48 1.67 0.54 0.84 0.66 1.23 2.05

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