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Variant classification

AVCG pathogenicity classifications

A citable reference table for variant pathogenicity across Dog, Cat, Horse. Every documented variant carrying a grade under the Animal Variant Classification Guidelines (AVCG; Boeykens, Broeckx et al. 2024), the ACMG/AMP-style framework for single-gene disorders in animals, curated in OMIA, here in one queryable place, each with its species, disease, HGVS, reference genome, and OMIA entry. Versioned: a classification updates as the evidence does.

Framework AVCG Source OMIA Cite How to cite API mcp.sniff.world/mcp/ · CC-BY 4.0

A grade exists only where the evidence does. The absence of one is not a verdict of benign, only that the work has not been done yet, and the AVCG withholds a call as a VUS rather than guess. 142 classified, growing; not a claim of completeness. A grade describes the documented variant's causality, not a prediction for any individual animal.

Grade
Species
Grade Species Disease OMIA
Pathogenic Cat Cardiomyopathy, hypertrophic, MYBPC3-related, autosomal dominantMondo↗ OMIA:002951
Pathogenic Cat Cardiomyopathy, hypertrophic, MYBPC3-related, autosomal recessiveMondo↗ OMIA:002952
Pathogenic Cat classical Ehlers-Danlos syndrome (cEDS), COL5A1-relatedMondo↗ OMIA:002165
Pathogenic Cat classical Ehlers-Danlos syndrome (cEDS), COL5A1-relatedMondo↗ OMIA:002165
Pathogenic Cat Dermatosparaxis Ehlers-Danlos syndrome (dEDS), ADAMTS2-relatedMondo↗ OMIA:000328
Pathogenic Cat Dihydropyrimidinase deficiencyMondo↗ OMIA:001776
Pathogenic Cat Epidermolysis bullosa, junctionalis, COL17A1-relatedMondo↗ OMIA:002793
Pathogenic Cat Factor XII deficiencyMondo↗ OMIA:000364
Pathogenic Cat Frontonasal dysplasia, ALX1-relatedMondo↗ OMIA:002717
Pathogenic Cat Gangliosidosis, GM2, type II (Sandhoff or variant 0)Mondo↗ OMIA:001462
Pathogenic Cat Gangliosidosis, GM2, type II (Sandhoff or variant 0)Mondo↗ OMIA:001462
Pathogenic Cat Gangliosidosis, GM2, type II (Sandhoff or variant 0)Mondo↗ OMIA:001462
Pathogenic Cat Glycogen storage disease IIMondo↗ OMIA:000419
Pathogenic Cat Glycogen storage disease IVMondo↗ OMIA:000420
Pathogenic Cat Haemophilia BMondo↗ OMIA:000438
Pathogenic Cat Hypohidrotic ectodermal dysplasia, X-linked, EDA-relatedMondo↗ OMIA:000543
Pathogenic Cat Hypotrichosis, HR-relatedMondo↗ OMIA:002229
Pathogenic Cat Mannosidosis, alphaMondo↗ OMIA:000625
Pathogenic Cat Methaemoglobinaemia, CYB5R3-relatedMondo↗ OMIA:002131
Pathogenic Cat Muscular dystrophy, Becker typeMondo↗ OMIA:001888
Pathogenic Cat Muscular dystrophy, Becker typeMondo↗ OMIA:001888
Pathogenic Cat Muscular dystrophy, Duchenne typeMondo↗ OMIA:001081
Pathogenic Cat Muscular dystrophy, Duchenne typeMondo↗ OMIA:001081
Pathogenic Cat Myotonia OMIA:000698
Pathogenic Cat Myotonia OMIA:000698
Pathogenic Cat Osteochondromatosis, EXT1-relatedMondo↗ OMIA:002554
Pathogenic Cat Porphyria, acute intermittentMondo↗ OMIA:001493
Pathogenic Cat Porphyria, acute intermittentMondo↗ OMIA:001493
Pathogenic Cat Porphyria, acute intermittentMondo↗ OMIA:001493
Pathogenic Cat Retinal degeneration IIMondo↗ OMIA:001244
Pathogenic Cat Vitamin D-deficiency rickets, type IBMondo↗ OMIA:002221
Pathogenic Dog Acyl-CoA dehydrogenase, medium chain, deficiency ofMondo↗ OMIA:002585
Pathogenic Dog Amelogenesis imperfecta, ACP4-relatedMondo↗ OMIA:002177
Pathogenic Dog Ataxia, cerebellar, ATP1B2-relatedMondo↗ OMIA:002110
Pathogenic Dog Bardet-Biedl syndrome 4Mondo↗ OMIA:002045
Pathogenic Dog Cleft lip with or without cleft palate, ADAMTS20-relatedMondo↗ OMIA:001140
Pathogenic Dog Darier diseaseMondo↗ OMIA:002265
Pathogenic Dog Dermatosparaxis Ehlers-Danlos syndrome (dEDS), ADAMTS2-relatedMondo↗ OMIA:000328
Pathogenic Dog Dermatosparaxis Ehlers-Danlos syndrome (dEDS), ADAMTS2-relatedMondo↗ OMIA:000328
Pathogenic Dog Episodic falling, BCAN-relatedMondo↗ OMIA:001592
Pathogenic Dog Exercise induced metabolic myopathyMondo↗ OMIA:002140
Pathogenic Dog Familial adenomatous polyposisMondo↗ OMIA:001916
Pathogenic Dog Glaucoma, primary open angle, ADAMTS10-relatedMondo↗ OMIA:001870
Pathogenic Dog Glaucoma, primary open angle, ADAMTS10-relatedMondo↗ OMIA:001870
Pathogenic Dog Glaucoma, primary open angle, ADAMTS17-relatedMondo↗ OMIA:001976
Pathogenic Dog Glaucoma, primary open angle, ADAMTS17-relatedMondo↗ OMIA:001976
Pathogenic Dog Glycogen storage disease IIIaMondo↗ OMIA:001577
Pathogenic Dog Hyperoxaluria, primary, type I (Oxalosis I)Mondo↗ OMIA:001672
Pathogenic Dog HypophosphatasiaMondo↗ OMIA:002162
Pathogenic Dog Ichthyosis, ABHD5-relatedMondo↗ OMIA:002368
Pathogenic Dog Intestinal cobalamin malabsorption, AMN-relatedMondo↗ OMIA:000565
Pathogenic Dog Intestinal cobalamin malabsorption, AMN-relatedMondo↗ OMIA:000565
Pathogenic Dog Lens luxationMondo↗ OMIA:000588
Pathogenic Dog Lipid malabsorption, ACSL5-relatedMondo↗ OMIA:002226
Pathogenic Dog Lysosomal storage disease, ARSG relatedMondo↗ OMIA:001503
Pathogenic Dog Mucopolysaccharidosis VIMondo↗ OMIA:000666
Pathogenic Dog Mucopolysaccharidosis VIMondo↗ OMIA:000666
Pathogenic Dog Mucopolysaccharidosis VIMondo↗ OMIA:000666
Pathogenic Dog Neuronal ceroid lipofuscinosis, 12Mondo↗ OMIA:001552
Pathogenic Dog Neutropenia, cyclicMondo↗ OMIA:000248
Pathogenic Dog Persistent Mullerian duct syndrome, AMHR2-relatedMondo↗ OMIA:002775
Pathogenic Dog Pontocerebellar hypoplasia, AMPD2-relatedMondo↗ OMIA:002838
Pathogenic Dog Recurrent inflammatory pulmonary diseaseMondo↗ OMIA:002205
Pathogenic Dog Respiratory distress syndrome, ANLN-relatedMondo↗ OMIA:002539
Pathogenic Dog Retinal atrophy - Cone-rod dystrophy 3Mondo↗ OMIA:001520
Pathogenic Dog Scott SyndromeMondo↗ OMIA:001353
Pathogenic Dog Stargardt disease 1Mondo↗ OMIA:002179
Pathogenic Dog Succinic semialdehyde dehydrogenase deficiencyMondo↗ OMIA:002250
Pathogenic Horse Androgen insensitivity syndrome (AIS)Mondo↗ OMIA:000991
Pathogenic Horse Androgen insensitivity syndrome (AIS)Mondo↗ OMIA:000991
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Pathogenic Horse Dwarfism, ACAN-relatedMondo↗ OMIA:001271
Pathogenic Horse Glycogen storage disease IVMondo↗ OMIA:000420
Pathogenic Horse Incontinentia pigmentiMondo↗ OMIA:001899
Pathogenic Horse Polysaccharide storage myopathy/PSSM1/Exertional rhabdomyolysisMondo↗ OMIA:001158
Pathogenic Horse ThrombastheniaMondo↗ OMIA:001000
Pathogenic Horse ThrombastheniaMondo↗ OMIA:001000
Likely pathogenic / pathogenic Cat Cardiomyopathy, hypertrophic, MYH7-relatedMondo↗ OMIA:002212
Likely pathogenic / pathogenic Cat classical Ehlers-Danlos syndrome (cEDS), COL5A1-relatedMondo↗ OMIA:002165
Likely pathogenic / pathogenic Cat Forebrain commissural malformation, ventriculomegaly and interhemispheric cysts, GDF7-related OMIA:002366
Likely pathogenic / pathogenic Cat Methaemoglobinaemia, CYB5R3-relatedMondo↗ OMIA:002131
Likely pathogenic / pathogenic Cat Methaemoglobinaemia, CYB5R3-relatedMondo↗ OMIA:002131
Likely pathogenic / pathogenic Cat Muscular dystrophy, Duchenne typeMondo↗ OMIA:001081
Likely pathogenic / pathogenic Cat Osteogenesis imperfecta, CREB3L1-relatedMondo↗ OMIA:002533
Likely pathogenic / pathogenic Cat Porphyria, acute intermittentMondo↗ OMIA:001493
Likely pathogenic / pathogenic Cat Porphyria, acute intermittentMondo↗ OMIA:001493
Likely pathogenic / pathogenic Dog Bardet-Biedl syndrome 2Mondo↗ OMIA:002484
Likely pathogenic / pathogenic Dog Geleophysic dysplasia, ADAMTSL2-relatedMondo↗ OMIA:001509
Likely pathogenic / pathogenic Dog Glaucoma, primary open angle, ADAMTS17-relatedMondo↗ OMIA:001976
Likely pathogenic / pathogenic Dog Ichthyosis, ASPRV1-relatedMondo↗ OMIA:002099
Likely pathogenic / pathogenic Dog Lens luxationMondo↗ · Glaucoma, primary open angle, ADAMTS17-relatedMondo↗ OMIA:000588
Likely pathogenic / pathogenic Dog Mucopolysaccharidosis VIMondo↗ OMIA:000666
Likely pathogenic / pathogenic Dog Neonatal encephalopathy with seizures, ATF2-relatedMondo↗ OMIA:001471
Likely pathogenic / pathogenic Dog Neurodegenerative vacuolar storage diseaseMondo↗ OMIA:001954
Likely pathogenic / pathogenic Dog Neuronal ceroid lipofuscinosis, 12Mondo↗ OMIA:001552
Likely pathogenic / pathogenic Dog Polyneuropathy, ARHGEF10-relatedMondo↗ OMIA:001917
Likely pathogenic / pathogenic Horse Androgen insensitivity syndrome (AIS)Mondo↗ OMIA:000991
Likely pathogenic / pathogenic Horse Androgen insensitivity syndrome (AIS)Mondo↗ OMIA:000991
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic / pathogenic Horse Dwarfism, ACAN-relatedMondo↗ OMIA:001271
Likely pathogenic / pathogenic Horse Dwarfism, ACAN-relatedMondo↗ OMIA:001271
Likely pathogenic Cat Epidermolysis bullosa, junctionalis, COL17A1-relatedMondo↗ OMIA:002793
Likely pathogenic Cat Wilson diseaseMondo↗ OMIA:001071
Likely pathogenic Dog Cardiomyopathy, dilated, ABCC9-relatedMondo↗ OMIA:002710
Likely pathogenic Dog Darier diseaseMondo↗ OMIA:002265
Likely pathogenic Horse Androgen insensitivity syndrome (AIS)Mondo↗ OMIA:000991
Likely pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely pathogenic Horse Dwarfism, ACAN-relatedMondo↗ OMIA:001271
Likely pathogenic Horse Night blindness, congenital stationary, GRM6-relatedMondo↗ OMIA:002692
Uncertain significance Cat Cardiomyopathy, hypertrophic, ALMS1-relatedMondo↗ OMIA:002316
Uncertain significance Cat Cardiomyopathy, hypertrophic, TNNT2-relatedMondo↗ OMIA:002304
Uncertain significance Cat Hypogonadotropic hypogonadism, TAC3-relatedMondo↗ OMIA:002219
Uncertain significance Cat Mucopolysaccharidosis VIMondo↗ OMIA:000666
Uncertain significance Dog Ichthyosis, ASPRV1-relatedMondo↗ OMIA:002099
Uncertain significance Horse Atlanto occipital fusion OMIA:000081
Uncertain significance Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Uncertain significance Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Uncertain significance / likely benign Horse Coat colour, dominant whiteMondo↗ OMIA:000209
Likely benign / benign Horse Coat colour, dominant whiteMondo↗ OMIA:000209
How to read these criteria

Each variant was classified independently by three or more reviewers. Each reviewer applied the AVCG criteria and assigned a grade, and the grades were then compared. Where reviewers agreed on the final grade, the individual criteria behind it were not necessarily reconciled. So the criteria shown here are the union of the reviewers' assessments: every criterion that at least one reviewer considered fulfilled, not a per-criterion consensus. The agreement is on the grade, not on each criterion.

Scope. The AVCG applies to single-gene disorders: variants in one gene with a high impact on disease risk, where one variant is sufficient (though not always fully penetrant) to cause disease. Grades follow the Animal Variant Classification Guidelines (AVCG; Boeykens, Broeckx et al. 2024, Front Vet Sci 11:1497817), an ACMG/AMP-style scheme; the species-specific feline application is validated in Boeykens et al. 2024 (Front Vet Sci 11:1327081; erratum 11:1458433). Classifications are curated in OMIA. Beyond the 142 graded variants, 6 are out-of-scope and 2 currently unresolved under the AVCG scope.

Evidence behind the grade. Where the OMIA-curated grade is independently corroborated by the published guideline, the variant carries a green Corroborated tag; open it for the supporting evidence (in-silico predictions, population genotype counts, mutant allele frequency, the human ortholog). 9 of the 142 are corroborated this way today, from the Boeykens, Broeckx et al. 2024 supplements (CC-BY); the remainder rest on a single curated source and show the grade alone, gaining evidence as it is added. Each variant's expanded view now shows the per-criteria AVCG breakdown in plain language, alongside the supporting evidence (see "How to read these criteria" below). Where sources disagree, the grade is flagged Contested and the disagreement shown, not overwritten.

Attribution. A grade is an AVCG classification curated in OMIA. Credit: AVCG (Boeykens et al. 2024) and OMIA. A grade describes the documented variant's causality, not a per-animal prediction: penetrance, modifier loci, and environment govern whether a carrier ever shows the phenotype.

In the knowledge graph. Each disease is cross-referenced to its canonical Mondo identifier (75 of the diseases here), so a classification links straight into the Monarch knowledge graph, where its human-disease analog and phenotypes live, the Mondo↗ link by each disease opens that term. Mondo is the cross-resource disease ontology (Vasilevsky, Mungall et al. 2025; CC-BY 4.0); the OMIA cross-references are Mondo's own curated mappings, OMIA remains the canonical source of the classification itself. Breed identifiers are reconciled to VBO, FCI, iDog and VeNom as a published SSSOM mapping set.

Query it. Built for pipelines and reference, not just reading: the same classifications are agent-callable through the Sniff MCP server (Streamable HTTP, mcp.sniff.world/mcp/) and the grounded Ask endpoint, returning the grade, its OMIA source, and how sure we are, cited.

References

Auto-generated from the sources of the classifications shown above.

  1. Boeykens F, ... Broeckx BJG, et al. Development and validation of animal variant classification guidelines. Front Vet Sci 2024;11:1497817. doi:10.3389/fvets.2024.1497817 · CC-BY-4.0
  2. Nicholas, F.W., Tammen, I., & Sydney Informatics Hub. (2026). Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org. doi:10.25910/2AMR-PV70. (Platform papers: Nicholas FW, NAR 2003 doi:10.1093/nar/gkg074; Lenffer J et al., NAR 2006 doi:10.1093/nar/gkj152.) · CC-BY-4.0
Last updated
Sources: AVCG: Boeykens, Broeckx et al. 2024, Front Vet Sci 11:1497817 (CC-BY) · Feline application: Boeykens et al. 2024, Front Vet Sci 11:1327081 (CC-BY) · Classifications curated in OMIA (omia.org) · Evidence behind the grade: Boeykens, Broeckx et al. 2024 supplements S5/S9 (CC-BY)