OMIA:001135-9913 : Renal dysplasia in Bos taurus (taurine cattle)

In other species: middle-African hedgehog , dog , domestic cat , horse

Categories: Renal / urinary system phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 248250 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2000

Species-specific name: Renal tubular dysplasia (RTD); Chronic interstitial nephritis with diffuse zonal fibrosis (CINF)

Species-specific symbol: RTD; CINF

History: The disorder was first described by Kuwamura et al. (1997)

Mapping: Two independent groups (Kobayashi et al., 2000; Ohba et al. 2000; Mammalian Genome 11:316-319) each used genome scans starting with more than 200 microsatellite markers to map the disorder to the central region of chromosome BTA1. Kobayashi et al. (2000) used a second set of 110 markers for fine-mapping, and then FISH-mapped a cosmid containing a relevant marker to BTA1q31-33. Ohba et al. (2000; Mammalian Genome 11:316-319) used homozygosity mapping to narrow the region to 4cM, and noted that this region is homologous to a region of human chromosome HSA3q that contains the gene paracellin-1 gene, mutations in which cause a related disorder in humans. Paracellin-1 thus became a comparative positional candidate gene.

Molecular basis: Building on the mapping results of Kobayashi et al. (2000) (see Mapping section above), Hirano et al. (2000) did some further fine mapping, and then constructed a cosmid library of the fine-mapped region of BTA1, and then used the best cosmid clone as a probe of kidney cDNA from normal and affected animals, identifying a single cDNA, which, when sequenced, turned out to be the bovine paracellin-1 gene, which they called Claudin-16, and which lacked exons 1-4 in affected animals. Independently, and building on the mapping results of Ohba et al. (2000; Mammalian Genome 11:316-319), Ohba et al. (2000; Genomics 68:229-236) did some further fine mapping and physical mapping of the region, and then identified and sequenced their comparative positional candidate gene, paracellin-1, revealing "a region of 37 kb including exons 1 to 4 of the bovine paracellin-1 gene was deleted in the affected animals". Thus both groups arrived at the same result at around the same time: the former paper was published in May 2000, and the latter in September 2000.

Breed: Japanese Black, Japan (Cattle) (VBO_0004987).
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
CLDN16 claudin 16 Bos taurus 1 NC_037328.1 (76869738..76847361) CLDN16 Homologene, Ensembl , NCBI gene


By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

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
648 Japanese Black, Japan (Cattle) Renal dysplasia CLDN16 Type 1 deletion, gross (>20) Naturally occurring variant 1 37kb deletion of exons 1-4 2000 10810088
781 Japanese Black, Japan (Cattle) Renal dysplasia CLDN16 Type 2 deletion, gross (>20) Naturally occurring variant 1 "a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" 200922: g. info moved to here (g.77528017_?) until can be standardised 2002 12047224 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:001135-9913: 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.

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.
2012 Testoni, S., Mazzariol, S., Drögemüller, C., Piffer, C., Aresu, L., Gentile, A. :
Renal dysplasia in grey Alpine breed cattle unrelated to CLDN16 mutations. Vet Rec 170(1):22, 2012. Pubmed reference: 22021062. DOI: 10.1136/vr.100209.
2006 Ohta, H., Adachi, H., Takiguchi, M., Inaba, M. :
Restricted localization of claudin-16 at the tight junction in the thick ascending limb of henle's loop together with claudins 3, 4, and 10 in bovine nephrons. J Vet Med Sci 68:453-63, 2006. Pubmed reference: 16757888.
2005 Nishii, N., Ohba, Y., Takasu, M., Katoh, K., Kitoh, K., Sasaki, Y., Kitagawa, H. :
Serum growth hormone and insulin-like growth factor-1 concentrations in Japanese black cattle with renal tubular dysplasia. J Vet Med Sci 67:399-402, 2005. Pubmed reference: 15876790.
Okada, K., Ishikawa, N., Fujimori, K., Goryo, M., Ikeda, M., Sasaki, J., Watanabe, D., Takasuga, A., Hirano, T., Sugimoto, Y. :
Abnormal development of nephrons in claudin-16-defective Japanese black cattle. J Vet Med Sci 67:171-8, 2005. Pubmed reference: 15750313.
2004 Hirayama, H., Kageyama, S., Moriyasu, S., Hirano, T., Sugimoto, Y., Kobayashi, N., Inaba, M., Sawai, K., Onoe, S., Minamihashi, A. :
Genetic diagnosis of claudin-16 deficiency and sex determination in bovine preimplantation embryos. J Reprod Dev 50:613-8, 2004. Pubmed reference: 15647612.
2002 Hirano, T., Hirotsune, S., Sasaki, S., Kikuchi, T., Sugimoto, Y. :
A new deletion mutation in bovine Claudin-16 (CL-16) deficiency and diagnosis Animal Genetics 33:118-122, 2002. Pubmed reference: 12047224.
Ohba, Y., Kitoh, K., Nakamura, H., Okuda, H., Kunieda, I., Sasaki, Y., Kitagawa, H. :
Renal reabsorption of magnesium and calcium by cattle with renal tubular dysplasia Veterinary Record 151:384-387, 2002. Pubmed reference: 12403519.
Sasaki, Y., Kitagawa, H., Kitoh, K., Okura, Y., Suzuki, K., Mizukoshi, M., Ohba, Y., Masegi, T. :
Pathological changes of renal tubular dysplasia in Japanese Black cattle Veterinary Record 150:628-632, 2002. Pubmed reference: 12046787.
Watanabe, D., Ban, A., Takahashi, M., Ishikawa, H., Watanabe, A., Yamanobe, H., Tunokane, S., Fujimore, K., Miyake, T., Okada, K., Otsuka, H., Oguro, M., Kawamura, S., Hirano, T., Sugimoto, Y., Abe, S., Saito, H. :
[Hereditary and clinico-pathological examinations of PCLN-1/Claudin-16 deficiency in Japanese Black cattle in the Tohoku region] Japanese Journal of Large Animal Clinics 25:1-10, 2002.
2001 Ohba, Y., Kitagawa, H., Kitoh, K., Oikawa, T., Sasaki, Y. :
Inheritance of renal tubular dysplasia in Japanese Black cattle Veterinary Record 149:153-154, 2001. Pubmed reference: 11517985.
Ohba, Y., Kitagawa, H., Okura, Y., Kitoh, K., Sasaki, Y. :
Clinical features of renal tubular dysplasia, a new hereditary disease in Japanese Black cattle Veterinary Record 149:115-118, 2001. Pubmed reference: 11504203.
2000 Hirano, T., Kobayashi, N., Itoh, T., Takasuga, A., Nakamaru, T., Hirotsune, S., Sugimoto, Y. :
Null mutation of PCLN-1/Claudin-16 results in bovine chronic interstitial nephritis Genome Research 10:659-663, 2000. Pubmed reference: 10810088.
Kobayashi, N., Hirano, T., Maruyama, S., Matsuno, H., Mukoujima, K., Morimoto, H., Noike, H., Tomimatsu, H., Hara, K., Itoh, T., Imakawa, K., Nakayama, H., Nakamaru, T., Sugimoto, Y. :
Genetic mapping of a locus associated with bovine chronic interstitial nephritis to chromosome 1 Animal Genetics 31:91-95, 2000. Pubmed reference: 10782206.
Ohba, Y., Kitagawa, H., Kitoh, K., Asahina, S., Nishimori, K., Yoneda, K., Kunieda, T., Sasaki, Y. :
Homozygosity mapping of the locus responsible for renal tubular dysplasia of cattle on bovine Chromosome 1 Mammalian Genome 11:316-319, 2000. Pubmed reference: 10754108.
Ohba, Y., Kitagawa, H., Kitoh, K., Sasaki, Y., Takami, M., Shinkai, Y., Kunieda, T. :
A deletion of the paracellin-1 gene is responsible for renal tubular dysplasia in cattle Genomics 68:229-236, 2000. Pubmed reference: 10995564. DOI: 10.1006/geno.2000.6298.
1999 Ushigaki, K., Uchida, K., Murakami, T., Yamaguchi, R., Tateyama, S. :
Multicystic renal dysplasia in a Japanese black bull Journal of Veterinary Medical Science 61:839-842, 1999. Pubmed reference: 10458111.
1997 Kuwamura, M., Kajimura, K., Yamate, J., Kotani, T., Tatesaki, R., Sakuma, S. :
Renal disease in young Japanese black cattle Journal of Comparative Pathology 116:101-106, 1997. Pubmed reference: 9076605.

Edit History

  • Created by Frank Nicholas on 01 Nov 2010
  • Changed by Frank Nicholas on 10 Aug 2011
  • Changed by Frank Nicholas on 30 Oct 2011
  • Changed by Frank Nicholas on 09 Dec 2011
  • Changed by Frank Nicholas on 04 Jan 2012
  • Changed by Frank Nicholas on 16 Sep 2012
  • Changed by Frank Nicholas on 17 Sep 2012
  • Changed by Imke Tammen2 on 17 Feb 2023