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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
HIST1H2BO ENST00000303806 29.83 96.81 64.68 1.05 0.23 0.51 1.59 0.19 1.32
PAQR8 ENST00000442253 29.84 39.78 32.97 1.05 0.65 0.86 1.59 1.66 1.67
TACO1 ENST00000258975 29.84 52.39 39.46 1.05 0.62 0.77 1.60 1.82 2.04
CIAPIN1 ENST00000394391 29.85 43.57 34.88 1.05 0.61 0.90 1.60 1.96 1.75
GGA1 ENST00000343632 29.85 3.11 14.20 1.05 3.45 1.99 1.60 0.28 0.60
VARS ENST00000375663 29.86 25.80 25.96 1.05 1.21 0.99 1.60 1.05 1.25
ARHGAP29 ENST00000260526 29.86 7.36 16.42 1.05 2.56 1.71 1.60 0.37 0.68
MAN1C1 ENST00000374332 29.87 20.60 23.35 1.05 1.44 1.20 1.60 0.76 0.99
VIP ENST00000367244 29.87 77.21 52.88 1.05 0.43 0.61 1.60 0.78 1.87
POC1B-GALNT4 ENST00000548729 29.88 27.01 26.57 1.05 1.23 0.99 1.60 1.12 1.25
MSX1 ENST00000382723 29.88 55.97 41.13 1.06 0.49 0.76 1.60 1.55 2.03
GRPEL2 ENST00000329271 29.89 61.56 44.14 1.06 0.54 0.61 1.60 1.41 2.03
SCN2B ENST00000278947 29.90 76.12 52.26 1.06 0.43 0.59 1.61 0.86 1.90
C18orf25 ENST00000282059 29.90 18.08 22.09 1.06 1.53 1.15 1.61 0.74 0.96
GRM4 ENST00000538487 29.91 11.51 18.71 1.06 2.11 1.57 1.61 0.57 0.81
CNTD1 ENST00000588408 29.91 38.10 32.23 1.08 0.77 0.91 1.60 1.69 1.60
HAUS4 ENST00000206474 29.92 30.98 28.60 1.08 1.04 0.80 1.60 1.36 1.35
PPFIA4 ENST00000272198 29.92 33.01 29.64 1.08 0.85 0.85 1.60 1.49 1.40
BICC1 ENST00000373886 29.93 14.90 20.53 1.08 1.94 1.48 1.60 0.62 0.89
RBL1 ENST00000373664 29.93 36.91 31.63 1.08 0.76 0.89 1.60 1.70 1.57
OSBPL3 ENST00000313367 29.94 28.13 27.17 1.08 1.19 0.99 1.60 1.20 1.25
NCSTN ENST00000294785 29.94 8.34 16.99 1.08 2.51 1.67 1.60 0.46 0.70
WBSCR22 ENST00000423497 29.95 39.26 32.78 1.08 0.70 0.85 1.59 1.64 1.64
LINC00998 ENST00000397764 29.95 87.94 59.12 1.08 0.25 0.51 1.59 0.37 1.68
RIMKLA ENST00000431473 29.96 55.85 41.11 1.08 0.51 0.76 1.59 1.58 2.04

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