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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
UTP11L ENST00000373014 34.98 62.29 47.40 0.92 0.53 0.65 1.85 1.33 1.87
BRD2 ENST00000395289 35.09 6.80 18.93 0.94 2.64 1.54 1.85 0.37 0.83
SRPR ENST00000332118 35.11 12.45 21.91 0.92 2.06 1.18 1.85 0.59 0.96
WDR54 ENST00000348227 35.16 72.09 53.04 0.91 0.52 0.61 1.85 1.04 1.86
SEZ6L ENST00000248933 35.16 17.30 24.25 0.91 1.61 1.10 1.85 0.75 1.05
UNC13D ENST00000207549 35.17 41.27 36.34 0.91 0.61 0.85 1.85 1.82 1.87
PYGM ENST00000164139 35.18 48.23 40.02 0.91 0.63 0.82 1.85 1.99 1.99
VGLL3 ENST00000398399 35.19 41.17 36.29 0.92 0.59 0.85 1.85 1.82 1.86
ZBTB9 ENST00000395064 35.19 39.74 35.60 0.92 0.66 0.86 1.85 1.66 1.77
MYOCD ENST00000425538 35.20 17.58 24.44 0.92 1.57 1.08 1.85 0.73 1.08
CAMSAP3 ENST00000446248 35.24 3.27 17.12 0.92 3.44 1.64 1.85 0.27 0.73
USP28 ENST00000003302 35.25 33.84 32.72 0.92 0.85 0.86 1.85 1.56 1.65
SYNPO ENST00000394243 35.25 12.60 22.03 0.92 2.09 1.16 1.85 0.58 0.97
APEX1 ENST00000216714 35.26 69.05 51.24 0.92 0.56 0.63 1.85 1.14 1.92
PGAP3 ENST00000300658 35.26 48.82 40.31 0.92 0.63 0.80 1.85 2.02 2.00
HSDL2 ENST00000398805 35.27 44.63 38.24 0.92 0.66 0.85 1.85 1.97 2.04
CDC14B ENST00000375241 35.27 15.19 23.32 0.92 1.90 1.19 1.85 0.67 0.98
TCP11L1 ENST00000334274 35.28 34.51 33.06 0.92 0.80 0.85 1.85 1.56 1.66
IL11RA ENST00000555003 35.28 81.24 58.31 0.92 0.34 0.49 1.85 0.54 1.64
ZC2HC1A ENST00000263849 35.29 17.00 24.15 0.92 1.63 1.11 1.85 0.73 1.05
FNDC5 ENST00000609187 35.29 43.70 37.73 0.92 0.62 0.84 1.85 1.96 2.01
FSHR ENST00000406846 35.30 62.27 47.57 0.92 0.53 0.65 1.85 1.34 1.89
GPX7 ENST00000361314 36.03 75.13 55.17 0.94 0.51 0.51 1.85 0.91 1.74
GDF6 ENST00000287020 36.04 7.40 19.77 0.94 2.53 1.49 1.85 0.39 0.85
GOLGA1 ENST00000373555 36.04 27.94 30.17 0.94 1.20 0.81 1.85 1.19 1.45

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