OMIA:002625-9913 : Skeletal dysplasia, FGD3-related in Bos taurus (taurine cattle)

Categories: Skeleton phene (incl. short stature & teeth) , Growth / size / body region phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 617554 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal incomplete dominant

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2015

Mapping: Takasuga et al. (2015): "Recessive skeletal dysplasia, characterized by joint- and/or hip bone-enlargement, was mapped within the critical region for a major quantitative trait locus (QTL) influencing carcass weight; previously named CW-3 in Japanese Black cattle."

Molecular basis: Takasuga et al. (2015): "To search for candidate causative variations for skeletal dysplasia and/or CW-3, three sires segregating the CW-3 QTL ... , three non-Q homozygous sires ... , and a Q-homozygous steer ... were subjected to targeted resequencing ... . The 3.3-Mb CW-3 region contained 910 candidate QTNs (858 SNPs and 52 indels), including four non-synonymous and five synonymous SNPs. ... . Non-synonymous SNPs were located in FGD3 ... and PTPDC1 ... . All non-synonymous SNPs showed strong association with carcass weight ... . The three non-synonymous SNPs in FGD3 showed complete linkage disequilibrium, while the linkage disequilibrium coefficient (r2) between the non-synonymous SNP in PTPDC1 and those in FGD3 was 0.907 in the GWAS population. ... the three non-synonymous SNPs in FDG3 caused loss of the start codon (ATG to ACG) and an amino acid substitution from His-171 (CAC) to Cys (TGC). Since the Kozak consensus sequence is present at the second Met of the 17th amino acid residue ... , the FGD3 variant probably produces an N-terminal 16 amino acid-truncated protein. ... the corresponding mutant protein showed reduced activity as a guanine nucleotide exchange factor for Cdc42." Sasaki et al. (2021) suggest that this variant (AC_000165.1:g.85826989_85826990dellinsTG, p.H171C in exon 2 of FGD3) was in close proximity of the JBH_8_1 haplotype region identified in their study. "However, the allele and the haplotype were not in LD with each other ... ; therefore, this variant was not a candidate for causative mutation in the JBH_8_1 haplotype region." Shibutani et al. (2023) conducted high-throughput screening of cattle variants and identified the FGD3 p.H171C (BTA8, g.85826989CA>TG) allele in Mishima cattle, but could not confirm the association with small chest width/depth reported by Takasuga et al. (2015), possibly due to small sample size of 72 Mishima cattle.

Clinical features: Takasuga et al. (2015): "Phenotypic characterization revealed that the risk allele causes disproportional tall stature and bone size that increases carcass weight in heterozygous individuals but causes disproportionately narrow chest width in homozygotes."

Breeds: Japanese Black, Japan (Cattle) (VBO_0004987), Mishima, Japan (Cattle) (VBO_0004993).
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
FGD3 FYVE, RhoGEF and PH domain containing 3 Bos taurus 8 NC_037335.1 (84356368..84420638) FGD3 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
1529 Japanese Black, Japan (Cattle) Skeletal dysplasia, FGD3 related FGD3 delins, small (<=20) Naturally occurring variant UMD_3.1.1 8 g.85826989_85826990delinsTG p.(H171C) 2015 26306008

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:002625-9913: Online Mendelian Inheritance in Animals (OMIA) [dataset].


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2023 Shibutani, S., Endo, M., Mizukami, K., Hosoi, E., Sakai, Y., Taniguchi, M., Harada, H., Momozawa, Y., Iwata, H. :
Development of a high-throughput screening method for the detection of 188 pathogenic variants and its application in Mishima cattle. Anim Genet 54:416-417, 2023. Pubmed reference: 36785519. DOI: 10.1111/age.13301.
2021 Sasaki, S., Watanabe, T., Ibi, T., Hasegawa, K., Sakamoto, Y., Moriwaki, S., Kurogi, K., Ogino, A., Yasumori, T., Wakaguri, H., Muraki, E., Miki, Y., Yoshida, Y., Inoue, Y., Tabuchi, I., Iwao, K., Arishima, T., Kawashima, K., Watanabe, M., Sugano, S., Sugimoto, Y., Suzuki, Y. :
Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle. Sci Rep 11:6687, 2021. Pubmed reference: 33758295. DOI: 10.1038/s41598-021-86225-y.
2015 Takasuga, A., Sato, K., Nakamura, R., Saito, Y., Sasaki, S., Tsuji, T., Suzuki, A., Kobayashi, H., Matsuhashi, T., Setoguchi, K., Okabe, H., Ootsubo, T., Tabuchi, I., Fujita, T., Watanabe, N., Hirano, T., Nishimura, S., Watanabe, T., Hayakawa, M., Sugimoto, Y., Kojima, T. :
Non-synonymous FGD3 variant as positional candidate for disproportional tall stature accounting for a carcass weight QTL (CW-3) and skeletal dysplasia in Japanese Black cattle. PLoS Genet 11:e1005433, 2015. Pubmed reference: 26306008. DOI: 10.1371/journal.pgen.1005433.

Edit History

  • Created by Imke Tammen2 on 17 Feb 2023
  • Changed by Imke Tammen2 on 17 Feb 2023