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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
SPESP1 ENST00000310673 97.20 86.66 94.65 0.10 0.24 0.09 0.11 0.40 0.11
C4orf6 ENST00000195455 97.79 97.44 99.29 0.11 0.22 0.11 0.11 0.19 0.04
BTN3A1 ENST00000289361 98.39 65.76 85.44 0.10 0.54 0.34 0.10 1.22 0.35
RP11-321M21.3 ENST00000578340 97.19 95.98 98.67 0.10 0.22 0.10 0.10 0.20 0.05
S100A9 ENST00000368738 97.79 80.35 91.83 0.11 0.37 0.14 0.10 0.59 0.17
FSCB ENST00000340446 98.39 97.59 99.50 0.10 0.22 0.11 0.10 0.20 0.05
LUZP4 ENST00000371920 97.78 92.00 97.49 0.11 0.23 0.08 0.10 0.33 0.07
BTN3A3 ENST00000244519 98.38 84.35 94.12 0.10 0.29 0.09 0.10 0.44 0.12
SIGLEC8 ENST00000321424 97.78 60.37 82.48 0.11 0.53 0.33 0.10 1.41 0.43
IBA57-AS1 ENST00000366713 98.38 98.65 99.74 0.10 0.20 0.12 0.10 0.15 0.04
TRIM49C ENST00000448984 97.77 77.79 90.85 0.11 0.42 0.15 0.10 0.79 0.20
MS4A6A ENST00000412309 98.37 96.30 99.15 0.10 0.22 0.11 0.10 0.19 0.04
LCN12 ENST00000371633 97.77 70.41 87.27 0.10 0.52 0.28 0.10 1.08 0.31
C14orf177 ENST00000325812 98.37 91.44 97.50 0.10 0.23 0.08 0.10 0.33 0.07
RLN2 ENST00000381627 97.76 93.36 98.00 0.10 0.28 0.09 0.10 0.28 0.05
ZNF83 ENST00000597597 98.36 98.54 99.57 0.10 0.20 0.12 0.10 0.15 0.05
AHNAK2 ENST00000333244 97.76 51.30 77.73 0.10 0.63 0.38 0.10 1.90 0.55
PYHIN1 ENST00000368140 97.75 69.75 86.95 0.10 0.53 0.28 0.10 1.13 0.30
PAGE2B ENST00000374971 98.36 93.21 98.16 0.10 0.28 0.09 0.10 0.30 0.05
CD33 ENST00000262262 97.75 71.72 87.85 0.10 0.51 0.24 0.10 1.07 0.32
ZNF69 ENST00000340180 98.35 91.25 97.40 0.10 0.23 0.08 0.10 0.34 0.07
ZNF766 ENST00000439461 97.74 90.02 96.67 0.10 0.25 0.08 0.10 0.37 0.08
PRR26 ENST00000441152 98.35 45.97 75.08 0.10 0.76 0.39 0.10 2.03 0.67
CEACAM21 ENST00000401445 97.74 86.08 94.64 0.10 0.27 0.09 0.10 0.44 0.11
KIAA1683 ENST00000392413 98.34 47.35 75.88 0.09 0.66 0.38 0.10 2.01 0.63

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