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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
SEMA6B ENST00000586582 67.67 23.25 43.81 0.57 1.43 0.61 1.07 0.92 2.01
HIST1H4C ENST00000377803 67.67 96.83 85.62 0.57 0.23 0.32 1.06 0.19 0.35
MDP1 ENST00000288087 67.68 77.04 75.26 0.57 0.42 0.37 1.05 0.78 0.67
GBP7 ENST00000294671 67.68 62.09 66.53 0.57 0.56 0.51 1.05 1.36 1.20
MARCH10 ENST00000311269 67.69 74.95 74.15 0.57 0.53 0.39 1.05 0.93 0.69
PLA2G3 ENST00000215885 67.69 65.52 68.60 0.57 0.53 0.47 1.05 1.23 1.05
NEIL3 ENST00000264596 67.70 61.30 66.18 0.57 0.54 0.52 1.04 1.39 1.20
FBXL12 ENST00000247977 67.70 43.38 55.12 0.57 0.61 0.51 1.04 1.95 1.73
AOC3 ENST00000308423 67.71 57.34 63.76 0.57 0.54 0.49 1.04 1.49 1.38
EVX2 ENST00000308618 67.71 36.41 51.14 0.57 0.82 0.65 1.04 1.63 1.90
PLA2G4F ENST00000382396 67.72 66.68 69.32 0.57 0.56 0.43 1.04 1.22 0.98
CSGALNACT1 ENST00000454498 67.72 71.41 72.24 0.57 0.53 0.43 1.03 1.05 0.82
RNF112 ENST00000461366 67.73 25.40 45.27 0.57 1.27 0.70 1.03 1.04 2.01
CD276 ENST00000318443 67.73 62.64 66.92 0.57 0.51 0.53 1.03 1.31 1.19
RABL2A ENST00000393167 67.74 83.71 79.01 0.57 0.27 0.39 1.03 0.47 0.53
KIAA0408 ENST00000483725 67.74 42.88 54.89 0.57 0.62 0.51 1.03 1.92 1.75
IER5 ENST00000367577 67.75 22.14 43.30 0.58 1.52 0.63 1.03 0.83 2.01
VWA3B ENST00000477737 67.75 50.45 59.36 0.58 0.65 0.51 1.03 1.95 1.69
OR10A3 ENST00000360759 67.76 91.53 82.99 0.58 0.23 0.32 1.03 0.32 0.40
NAALADL2 ENST00000454872 67.77 38.90 52.63 0.58 0.70 0.61 1.03 1.65 1.89
TALDO1 ENST00000319006 67.77 61.87 66.48 0.58 0.57 0.51 1.03 1.35 1.22
IL19 ENST00000340758 67.78 70.76 71.84 0.58 0.48 0.44 1.03 1.08 0.82
KCNE1L ENST00000372101 67.78 90.07 82.29 0.58 0.25 0.34 1.03 0.37 0.45
LIPN ENST00000404459 67.79 47.22 57.42 0.58 0.66 0.51 1.03 2.01 1.67
CEP104 ENST00000378230 67.79 37.92 52.09 0.59 0.80 0.61 1.03 1.70 1.93

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