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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
OR2L3 ENST00000359959 89.07 99.12 96.94 0.19 0.15 0.08 0.32 0.14 0.07
OR14A16 ENST00000357627 98.48 99.12 99.68 0.10 0.15 0.12 0.11 0.14 0.04
C14orf132 ENST00000555004 92.66 99.13 98.40 0.15 0.15 0.10 0.18 0.14 0.05
AC112693.2 ENST00000599897 92.66 99.13 97.72 0.15 0.15 0.09 0.17 0.14 0.05
PBOV1 ENST00000527246 97.37 99.14 99.62 0.10 0.15 0.12 0.11 0.14 0.05
FAM220A ENST00000313324 95.87 99.14 99.28 0.11 0.15 0.11 0.11 0.14 0.04
VN1R4 ENST00000311170 96.06 99.15 99.32 0.11 0.15 0.11 0.11 0.14 0.04
EDDM3B ENST00000326783 95.96 99.15 99.30 0.11 0.15 0.11 0.11 0.14 0.04
BIRC8 ENST00000426466 95.26 99.16 99.12 0.10 0.15 0.11 0.11 0.14 0.04
C10orf40 ENST00000521074 92.72 99.16 97.13 0.15 0.15 0.08 0.17 0.14 0.07
AL136115.1 ENST00000391369 92.72 99.17 98.12 0.15 0.15 0.09 0.17 0.14 0.05
AC114546.1 ENST00000391457 92.73 99.17 98.45 0.15 0.15 0.10 0.17 0.14 0.05
SMCP ENST00000368765 99.47 99.18 99.95 0.11 0.15 0.13 0.13 0.14 0.04
CTC-241N9.1 ENST00000499601 91.19 98.30 97.67 0.15 0.21 0.09 0.21 0.14 0.06
IFNA16 ENST00000380216 95.63 98.74 99.26 0.11 0.16 0.11 0.11 0.14 0.04
H2AFB1 ENST00000354461 95.48 98.30 98.97 0.11 0.21 0.10 0.11 0.14 0.04
AC007405.2 ENST00000409786 92.03 98.75 97.19 0.15 0.16 0.08 0.20 0.14 0.06
RBMXL3 ENST00000424776 88.54 98.31 96.27 0.20 0.21 0.07 0.34 0.14 0.09
KRTAP20-2 ENST00000330798 82.97 98.76 93.76 0.30 0.16 0.10 0.55 0.14 0.13
C5orf55 ENST00000408966 95.69 98.31 99.05 0.11 0.21 0.11 0.12 0.14 0.04
NPIPA2 ENST00000553201 92.04 98.76 98.21 0.15 0.16 0.09 0.20 0.14 0.05
EBLN1 ENST00000422359 99.25 98.32 99.74 0.11 0.21 0.12 0.12 0.14 0.04
NHLRC4 ENST00000424439 92.04 98.77 98.11 0.15 0.16 0.09 0.20 0.14 0.05
AC007421.1 ENST00000593717 91.26 98.32 98.60 0.15 0.21 0.10 0.21 0.14 0.05
OR8D1 ENST00000357821 95.24 98.77 98.88 0.10 0.16 0.10 0.11 0.14 0.04

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