OMIA:002606-9615 : Skeletal dysplasia 3, PCYT1A-related in Canis lupus familiaris (dog)

Categories: Skeleton phene (incl. short stature & teeth)

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 123695 (gene) , 608940 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2022

Species-specific name: Skeletal dysplasia 3; disproportionate dwarfism

Species-specific symbol: SD3

Species-specific description: Skeletal dysplasia 3 (SD3) is a moderately severe form of disproportionate dwarfism in Vizslas. Affected dogs have short legs and their shoulder height is reduced by ~11 cm compared to non-affected dogs. Skeletal dysplasia represents a highly heterogenoues group of diseases with more than 400 distinct entitities described in humans.

Mapping: Ludwig-Peisker et al. (2022) performed linkage mapping in a single family with two affected and two unaffected offspring and homozygosity mapping in six affected dogs. The intersection of the linked and homozygous intervals resulted in two closely neighbouring segments on chromosome 33 that together spanned ~4 Mb. The exact boundaries of the critical intervals were Chr33:26,941,791-28,331,855 and Chr33:29,015,236-31,008,198 (UU_Cfam_GSD_1.0 assembly).

Molecular basis: By whole-genome resequencing of one of the affected dogs at 19.9x coverage and comparing the data to 926 control genomes, Ludwig-Peisker et al. (2022) identified a single private homozygous protein changing variant in the cirtical interval on chromosome 33. "This variant affected the PCYT1A gene encoding phosphate cytidylyltransferase 1A, choline, which has also been termed choline-phosphate cytidylyltransferase-α. The genomic variant designation is Chr33:30,067,814:g.A>G (UU_Cfam_GSD_1.0 assembly). It represents a missense variant, XM_038583131.1:c.673T>C, predicted to cause an exchange of a highly conserved amino acid in the PCYT1A protein XP_038439059.1:p.(Y225H)." The genotypes at this variant showed perfect genotype-phenotype association in a cohort of 7 cases and 123 unaffected Vizslas. However, Ludwig-Peisker et al. (2022) encountered one additional Vizsla affected by disproportional dwarfism that was homozygous for the wildtype allele at the PCYT1A variant. In contrast to the 7 other cases from the study, this dog had a marked brachygnathia inferior in addition to the short legs. Ludwig-Peisker et al. (2022) hypothesized that the phenotype in this dog may have been caused by another genetic variant and that heterogeneity provides a plausible explanation for the discordant genotype in this dog.

Clinical features: Ludwig-Peisker et al. (2022) measured shoulder heights in 29 adult Vizslas that had been genotyped for the PCYT1A:p.Y225H variant. The shoulder height in 7 homozygous mutant dogs was highly variable. On average, homozygous mutant dogs were ~11 cm shorter than dogs with at least one wildtype PCY1A allele. Ludwig-Peisker et al. (2022) found no size differences between homozygous wildtype and heterozygous dogs. Radiographs of affected dogs showed shortened and thickened radius and ulna with procurvatum and varus deformity. The humerus in an affected dog was also markedly shortened with flattened articular surfaces. Similar changes were seen in the hind limbs with marked shortening and deformity of the femur resulting in subluxation of the hip joint and secondary deformity of the acetabula. So far, no clinically overt consequences such as osteoarthritis and lameness due to the skeletal changes have been observed in the affected dogs. However, the oldest affected dog in Ludwig-Peisker et al. (2022) was only 7 years old. Human patients with PCYT1A variants are affected by spondylometaphyseal dysplasia with cone-rod dystrophy and develop an early-onset progressive visual impairment associated with a pigmentary maculopathy and cone-rod dysfunction. The ophthalmologic examination of a single affected Vizsla at seven years of age did not reveal any signs of cone-rod dystrophy (Ludwig-Peisker et al. 2022).

Breed: Vizsla (Dog) (VBO_0201389).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
PCYT1A phosphate cytidylyltransferase 1, choline, alpha Canis lupus familiaris 33 NC_051837.1 (29648017..29596717) PCYT1A Homologene, Ensembl , NCBI gene


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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
1515 Vizsla (Dog) skeletal dysplasia 3 PCYT1A missense Naturally occurring variant UU_Cfam_GSD_1.0 33 g.30067814A>G c.673T>C p.Y225H XM_038583131.1; XP_038439059.1 2022 36553621

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:002606-9615: Online Mendelian Inheritance in Animals (OMIA) [dataset].


2022 Ludwig-Peisker, O., Ansel, E., Schweizer, D., Jagannathan, V., Loechel, R., Leeb, T. :
PCYT1A missense variant in Vizslas with disproportionate dwarfism. Genes (Basel) 13:2354, 2022. Pubmed reference: 36553621. DOI: 10.3390/genes13122354.

Edit History

  • Created by Tosso Leeb on 20 Dec 2022
  • Changed by Tosso Leeb on 20 Dec 2022
  • Changed by Imke Tammen2 on 25 May 2024