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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
CHTF8 ENST00000448552 25.10 57.13 39.45 1.37 0.56 0.77 1.15 1.50 2.05
BMF ENST00000354670 25.64 56.95 39.66 1.33 0.56 0.80 1.20 1.53 2.05
KCNJ5 ENST00000529694 25.95 59.79 41.08 1.37 0.52 0.76 1.22 1.37 2.05
SEC22A ENST00000309934 26.15 65.30 44.17 1.35 0.51 0.61 1.26 1.24 2.05
BOLA3 ENST00000327428 27.28 58.43 41.05 1.21 0.54 0.75 1.41 1.38 2.05
TWSG1 ENST00000262120 27.47 55.11 39.66 1.23 0.58 0.80 1.42 1.63 2.05
GEMIN2 ENST00000308317 28.06 53.06 38.87 1.16 0.66 0.80 1.48 1.77 2.05
SLC35D3 ENST00000331858 29.27 51.83 38.85 1.09 0.61 0.81 1.58 1.87 2.05
ATP6V1B1 ENST00000234396 29.64 50.80 38.49 1.06 0.63 0.84 1.54 1.93 2.05
CD53 ENST00000271324 29.69 55.17 40.63 1.06 0.57 0.81 1.57 1.61 2.05
EDAR ENST00000258443 30.74 50.95 39.22 0.96 0.65 0.78 1.63 1.93 2.05
BLOC1S1 ENST00000548925 31.27 54.51 41.11 0.96 0.59 0.76 1.68 1.65 2.05
ARHGAP19-SLIT1 ENST00000453547 32.78 52.71 40.96 0.95 0.67 0.77 1.70 1.80 2.05
GINS4 ENST00000276533 32.81 58.63 44.18 0.94 0.54 0.62 1.70 1.42 2.05
STK3 ENST00000523601 33.54 48.19 39.22 0.92 0.63 0.78 1.70 1.99 2.05
MCM8 ENST00000378896 33.56 51.45 40.64 0.95 0.63 0.81 1.70 1.89 2.05
SAMHD1 ENST00000262878 34.49 51.03 40.96 1.00 0.65 0.77 1.80 1.92 2.05
TIE1 ENST00000372476 34.62 50.22 40.61 0.97 0.67 0.81 1.79 1.99 2.05
ZBTB8B ENST00000609129 34.94 47.64 39.64 0.94 0.61 0.80 1.85 1.97 2.05
SKIV2L ENST00000375394 35.04 47.60 39.65 0.92 0.62 0.80 1.87 1.99 2.05
FKTN ENST00000223528 35.10 45.99 38.86 0.92 0.77 0.80 1.85 2.02 2.05
TGIF1 ENST00000330513 35.33 49.75 40.70 0.92 0.66 0.81 1.87 2.03 2.05
VKORC1 ENST00000394975 35.62 56.52 44.58 0.97 0.52 0.62 1.89 1.53 2.05
RMI1 ENST00000325875 36.38 48.93 40.84 0.96 0.65 0.80 1.81 2.04 2.05
ZNF329 ENST00000598312 36.66 48.86 40.98 0.95 0.63 0.76 1.76 2.03 2.05

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