Variant interpretation powered by comparative genomics

Eliminate tolerated missense noise so you can focus faster

CodeXome maps 80 million years of primate evolution onto every human protein-coding gene. Reduce manual review by 72%, reclassify variants with deep-time biological evidence, and reach stronger clinical conclusions faster.

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177k+ VUS reclassified as likely benign using CodeXome

BRCA2

ATM

APC

NF1

POLE

BRCA1

PLEC

TSC2

RYR2

MSH6

RYR1

ALMS1

USH2A

DICER1

ADGRV1

DMD

PRKDC

PALB2

BRIP1

ALK

FLNC

DSP

RECQL4

MYH7

MSH2

VPS13B

RAD50

FBN1

NSF-Funded Research Platform

NSF-Funded Comparative Genomics Research

CodeXome adds the layer modern genomics has always been missing: 80 million years of primate evolution, mapped variant-by-variant onto human genes.

Population frequencies show what exists in humans.
Evolution reveals what biology allowed.

72%

Reduction in manual review when recurrence filters benign variation.

~2B

Evolutionary datapoints aggregated across primates.

~2M

Observed amino-acid substitutions mapped to human GRCh38.

Start with a complete evolutionary framework

CodeXome delivers deep-time biology, gene-level alignment, and automated interpretation tools out-of-the-box—no setup required.

Table showing genetic base pairs for humans, great apes, gibbons, old world monkeys, new world monkeys, tarsiers, lemures, and pottos, with humans having bases A, A, A, G, G, A, T, C and gibbons showing N, N, N and C.

The evolutionary record, quantified

CodeXome aggregates primate exomes into a unified multi-species alignment, mapping millions of amino-acid substitutions to human GRCh38 coordinates.

Histogram showing the number of genes versus total branch length of gene tree in substitutions per site, with most genes centered around 0.5 to 1.0 substitutions per site.

Every gene, mapped across evolution

Constraint patterns, tolerated substitutions, domain-level conservation, and human-unique changes presented in one interpretable profile.

User interface with search bars labeled UniProt, Clinical Variants, and gnomAD, showing color-coded circular indicators representing Clinical Variants and CodeXome Annotations (NT).

Evidence-backed interpretation

Automatically apply recurrence, absence, evolutionary tolerance, ClinVar/UniProt/gnomAD overlays, and primate-weighted scoring.

Why evolution matters

Function-first evidence for every coding gene

Comparative genomics exposes biochemical, structural, and evolutionary patterns that population datasets cannot reveal.

Uncover tolerated variation
See which amino-acid changes appear naturally across primate species—revealing benign biochemical flexibility.

Expose functional constraint
Positions unchanged across 80M+ years highlight domains where mutation is not tolerated.

12% Amino Acid VUS for SCN5A reclassified to likely benign in one step.

Case Studies

Explore CodeXome’s evolutionary tools

Phylogenetic tree and multiple sequence alignment of primate species showing amino acid variations at positions 1147 to 1186.

Evolutionary alignment reimagined

CodeXome synchronizes primate exomes to human coordinates, giving you residue-level constraint and tolerance with a clarity no population dataset can reach.

Functional insight at a glance

Domain boundaries, motifs, IDRs, conserved regions, human-unique mutations—all delivered in one unified interface.

Table showing variant counts: 55,805 original rows and total variants evaluated, 20,523 variants retained. CodeXome data lists 8,735 genes with information, 5,019 private variants, and 15,504 shared variants.

Evidence that resolves uncertainty

Absence, recurrence, tolerance, and constraint all surfaced instantly for any variant.

Two labeled boxes on a grid background showing scores and outcomes: 'Score: 0.944, Outcome: Pathogenic, Confidence: High' and 'Score: 0.299, Outcome: Benign, Confidence: Medium'.

Interpretation meets intelligence

ML-assisted scoring trained on deep-time biological signal, not population bias.

Let us show you CodeXome

Deeper evidence. Faster interpretation. Stronger conclusions.

See how evolutionary biology transforms variant interpretation.

Evolution-first interpretation reduced review time by 72%.

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