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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
HPS5 ENST00000349215 39.39 36.69 36.21 0.89 0.77 0.87 1.77 1.66 1.84
PGRMC1 ENST00000217971 39.39 43.00 39.52 0.89 0.61 0.80 1.77 1.90 2.03
QTRTD1 ENST00000485050 39.40 63.72 50.59 0.89 0.49 0.66 1.78 1.22 1.86
GUCY2C ENST00000261170 39.40 59.83 48.49 0.89 0.52 0.68 1.78 1.36 1.86
LCLAT1 ENST00000309052 39.41 42.93 39.50 0.89 0.63 0.80 1.78 1.90 2.03
ZBTB3 ENST00000394807 39.41 37.23 36.44 0.90 0.77 0.84 1.78 1.66 1.88
ZNF366 ENST00000318442 39.42 26.13 31.01 0.90 1.20 0.82 1.78 1.09 1.52
CRYGS ENST00000392499 39.42 53.00 44.85 0.90 0.66 0.67 1.78 1.77 2.04
C11orf70 ENST00000434758 39.43 64.94 51.28 0.90 0.48 0.63 1.78 1.24 1.92
STEAP4 ENST00000380079 39.43 56.29 46.53 0.90 0.52 0.66 1.78 1.55 1.90
MANEAL ENST00000373045 39.44 46.05 40.95 0.90 0.77 0.77 1.78 2.04 2.06
CRAT ENST00000318080 39.45 54.78 45.82 0.90 0.57 0.67 1.78 1.64 1.97
RCVRN ENST00000226193 39.45 92.69 68.01 0.90 0.29 0.51 1.78 0.30 1.10
TNNT3 ENST00000278317 39.46 48.57 42.28 0.90 0.65 0.70 1.78 2.01 2.01
C12orf5 ENST00000179259 39.46 28.43 32.13 0.90 1.16 0.89 1.78 1.24 1.60
UBE2V2 ENST00000523111 39.47 69.28 53.80 0.90 0.57 0.62 1.77 1.14 1.79
KIAA1644 ENST00000381176 39.47 51.25 43.72 0.90 0.65 0.61 1.77 1.90 2.02
LEMD3 ENST00000308330 39.48 9.20 22.51 0.91 2.47 1.16 1.77 0.47 0.97
ABHD4 ENST00000428304 39.48 59.24 48.22 0.91 0.49 0.66 1.77 1.44 1.87
C4orf33 ENST00000281146 39.49 76.92 58.26 0.91 0.43 0.47 1.77 0.79 1.65
PIK3R3 ENST00000262741 39.49 54.97 45.94 0.91 0.57 0.70 1.77 1.63 1.97
TMEM2 ENST00000377044 39.50 32.47 34.26 0.91 0.86 0.87 1.77 1.48 1.76
SLC22A3 ENST00000275300 39.50 54.85 45.87 0.91 0.57 0.70 1.76 1.63 1.97
NAT10 ENST00000257829 39.51 50.20 43.22 0.91 0.67 0.65 1.76 1.99 1.99
TUBD1 ENST00000325752 39.51 48.26 42.15 0.91 0.63 0.70 1.76 1.99 2.01

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