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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
MFHAS1 ENST00000276282 55.66 43.70 48.57 0.59 0.62 0.67 1.66 1.96 1.85
ZNF276 ENST00000443381 55.66 42.07 47.68 0.59 0.61 0.66 1.66 1.85 1.88
VAT1L ENST00000302536 55.67 60.38 58.08 0.59 0.53 0.47 1.66 1.41 1.65
TMIE ENST00000326431 55.67 89.93 75.80 0.59 0.25 0.38 1.66 0.37 0.63
MED9 ENST00000268711 55.68 50.31 52.24 0.59 0.66 0.59 1.66 1.96 1.90
TRAPPC13 ENST00000438419 55.68 37.62 45.36 0.59 0.78 0.70 1.66 1.71 2.00
SYCP2L ENST00000283141 55.69 53.94 54.37 0.59 0.65 0.58 1.66 1.70 1.75
CLDN16 ENST00000264734 55.69 40.44 46.80 0.59 0.62 0.67 1.66 1.77 1.87
DPH1 ENST00000263083 55.70 71.95 65.30 0.59 0.51 0.53 1.66 1.07 1.31
APOA2 ENST00000367990 55.70 86.06 73.69 0.59 0.27 0.42 1.66 0.43 0.71
OTP ENST00000306422 55.71 14.85 33.41 0.59 1.92 0.87 1.65 0.62 1.71
VAMP8 ENST00000263864 55.72 67.07 62.21 0.59 0.54 0.48 1.65 1.23 1.44
FOXD1 ENST00000499003 55.72 43.89 48.68 0.59 0.61 0.68 1.65 1.96 1.85
CTRL ENST00000574481 55.73 81.52 71.03 0.59 0.33 0.43 1.64 0.53 0.85
MPHOSPH10 ENST00000244230 55.73 16.58 34.39 0.58 1.77 0.90 1.64 0.71 1.77
ARNTL2 ENST00000266503 55.74 47.27 50.53 0.58 0.66 0.67 1.63 2.01 1.86
SLC37A2 ENST00000308074 55.74 63.25 59.91 0.58 0.47 0.49 1.64 1.31 1.63
SUN2 ENST00000405018 55.75 32.69 42.49 0.58 0.85 0.68 1.64 1.45 2.00
KRT15 ENST00000254043 55.75 81.18 70.81 0.58 0.35 0.43 1.64 0.55 0.87
ACCS ENST00000263776 55.76 44.63 49.11 0.58 0.66 0.72 1.64 1.97 1.83
CCDC181 ENST00000545005 55.76 57.72 56.55 0.58 0.57 0.52 1.64 1.46 1.70
RPS6KL1 ENST00000555647 55.77 46.67 50.24 0.58 0.75 0.65 1.64 1.97 1.91
P2RY14 ENST00000309170 55.77 65.34 61.21 0.58 0.52 0.43 1.63 1.25 1.49
TIMM10B ENST00000254616 55.78 94.82 78.52 0.58 0.23 0.38 1.63 0.24 0.55
PCSK6 ENST00000348070 55.78 38.04 45.64 0.58 0.77 0.68 1.63 1.71 1.98

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