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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
HARS2 ENST00000230771 40.75 40.30 38.83 0.87 0.62 0.82 1.75 1.75 2.04
SEMA4G ENST00000210633 40.88 41.69 39.64 0.84 0.61 0.80 1.73 1.80 2.04
ZCCHC9 ENST00000254037 41.35 50.16 44.23 0.84 0.67 0.62 1.68 1.99 2.04
GABPB2 ENST00000368918 41.40 43.92 40.83 0.82 0.61 0.80 1.68 1.97 2.04
MATN1 ENST00000373765 41.46 44.16 41.03 0.82 0.61 0.76 1.68 1.95 2.04
UBA7 ENST00000333486 41.75 50.62 44.81 0.80 0.63 0.66 1.73 1.95 2.04
LACE1 ENST00000368977 41.99 50.43 44.84 0.80 0.65 0.67 1.75 1.95 2.04
GFOD2 ENST00000268797 42.14 43.15 40.82 0.78 0.62 0.80 1.75 1.90 2.04
HBG2 ENST00000380259 42.21 50.49 45.00 0.78 0.65 0.70 1.75 1.94 2.04
ITGA1 ENST00000282588 42.30 37.51 38.23 0.76 0.78 0.85 1.75 1.66 2.04
GCC1 ENST00000321407 42.92 42.77 41.05 0.81 0.62 0.76 1.77 1.92 2.04
LGR5 ENST00000266674 42.94 38.83 39.27 0.81 0.68 0.80 1.77 1.66 2.04
SNX5 ENST00000377768 43.15 36.64 38.20 0.82 0.77 0.85 1.79 1.65 2.04
IKBKAP ENST00000374647 43.70 38.25 39.35 0.76 0.76 0.78 1.78 1.70 2.04
PLSCR1 ENST00000342435 44.11 35.66 38.20 0.71 0.78 0.85 1.78 1.58 2.04
HPD ENST00000289004 44.28 35.43 38.13 0.68 0.77 0.86 1.77 1.56 2.04
TIMM17A ENST00000367287 44.58 35.44 38.32 0.65 0.77 0.85 1.80 1.56 2.04
CARNS1 ENST00000445895 44.70 47.69 44.79 0.65 0.61 0.66 1.77 1.97 2.04
ESRP2 ENST00000473183 44.94 37.69 39.68 0.63 0.78 0.80 1.74 1.70 2.04
HCRTR1 ENST00000403528 45.08 46.94 44.55 0.65 0.71 0.62 1.74 1.94 2.04
HABP4 ENST00000375249 45.26 36.93 39.44 0.63 0.75 0.77 1.75 1.70 2.04
VPS37B ENST00000267202 45.33 34.72 38.33 0.62 0.78 0.85 1.75 1.54 2.04
NOA1 ENST00000264230 45.42 39.67 40.70 0.58 0.68 0.81 1.76 1.66 2.04
USP16 ENST00000334352 45.43 40.24 41.04 0.57 0.61 0.76 1.76 1.73 2.04
TBC1D2B ENST00000300584 45.73 36.30 39.39 0.58 0.82 0.78 1.77 1.61 2.04

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