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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
SLC36A1 ENST00000243389 31.64 47.54 37.84 0.95 0.62 0.85 1.70 2.02 2.01
C12orf44 ENST00000336854 31.65 33.88 31.00 0.96 0.84 0.82 1.70 1.55 1.52
CLASRP ENST00000221455 31.65 17.86 22.91 0.95 1.51 1.19 1.70 0.72 0.98
HUNK ENST00000270112 31.66 10.93 19.29 0.95 2.10 1.52 1.70 0.51 0.85
RANBP2 ENST00000283195 31.66 2.60 14.91 0.95 3.55 1.92 1.70 0.29 0.63
CPNE8 ENST00000331366 31.67 21.29 24.54 0.95 1.42 1.06 1.70 0.81 1.08
NUP107 ENST00000229179 31.67 29.31 28.66 0.95 1.14 0.80 1.70 1.36 1.34
ASNS ENST00000175506 31.68 40.25 34.22 0.95 0.61 0.87 1.70 1.73 1.77
MANEA ENST00000358812 31.68 45.69 36.89 0.95 0.75 0.81 1.70 2.01 1.94
SEC24D ENST00000280551 31.69 31.28 29.65 0.95 0.99 0.85 1.70 1.38 1.39
COMP ENST00000222271 31.69 41.07 34.60 0.95 0.59 0.90 1.70 1.80 1.77
TBL1X ENST00000217964 31.70 13.02 20.47 0.95 2.07 1.49 1.71 0.59 0.89
SLC30A10 ENST00000366926 31.70 9.93 18.84 0.95 2.32 1.56 1.71 0.50 0.83
GET4 ENST00000265857 31.71 24.68 26.32 0.95 1.29 1.00 1.71 1.04 1.25
VPS28 ENST00000377348 31.71 39.83 33.94 0.95 0.65 0.90 1.71 1.68 1.73
MED28 ENST00000237380 31.72 74.15 52.17 0.96 0.53 0.61 1.71 1.03 1.90
OGG1 ENST00000302036 31.72 73.53 51.78 0.96 0.53 0.62 1.71 1.03 1.93
PDE7A ENST00000401827 31.73 30.61 29.34 0.96 1.08 0.82 1.71 1.39 1.35
ESCO2 ENST00000305188 31.73 45.47 36.79 0.96 0.70 0.82 1.71 1.99 1.94
PTCHD4 ENST00000339488 31.74 35.18 31.67 0.96 0.76 0.89 1.71 1.58 1.59
GLE1 ENST00000309971 31.74 41.04 34.61 0.96 0.59 0.90 1.71 1.81 1.77
RAB3B ENST00000371655 31.75 40.29 34.31 0.96 0.62 0.87 1.71 1.74 1.76
IFT52 ENST00000373030 31.75 45.76 36.97 0.96 0.75 0.78 1.71 2.02 1.94
GPD1 ENST00000301149 31.76 45.27 36.66 0.96 0.70 0.84 1.71 1.97 1.93
GPC6 ENST00000377047 31.76 25.64 26.88 0.96 1.24 0.97 1.71 1.05 1.27

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