OMIA:002435-9823 : Sperm, short tail, SPEF2-related in Sus scrofa (pig)

Categories: Reproductive system phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 610172 (gene) , 618751 (trait)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2006

Species-specific name: Immotile short-tail sperm defect; Sterilizing short-tail sperm defect

Species-specific symbol: ISTS

Species-specific description: "The ISTS phenotype is characterized as lowered sperm counts, short sperm tails, and axonemal abnormalities" (Sironen et al., 2006)

Inheritance: Autosomal recessive, sex-limited

Molecular basis: "Sequence analysis of a candidate gene KPL2 revealed the presence of an inserted retrotransposon within an intron. The insertion affects splicing of the KPL2 transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation." (Sironen et al., 2006) The KPL2 gene is now called SPEF2 (sperm flagellar 2). Sironen et al. (2014) “analyzed the expression of the genomic region adjacent to the L1 insertion on porcine chromosome 16. Based on the RNA-seq data analysis, prolactin receptor (PRLR) was identified as down-regulated in the oviduct of ISTS homozygous sows. Quantitative PCR (qPCR) analysis confirmed the significant down-regulation of PRLR in the ovary, oviduct, and uterus of ISTS homozygous and carrier sows compared with controls. In addition, three unannotated loci between PRLR and SPEF2 showed some transcription activity in the analyzed samples. …. The current data suggest that the presence of the L1 affects by some mechanism the expression patterns upstream of the insertion site.”

Clinical features: Homozygous boars are eliminated from the population due to infertility. Sironen et al. (2012) “investigated the association of the L1 insertion and PRLR haplotype with reproduction traits in the Finnish Yorkshire population. ….. The L1-insertion within SPEF2 gene was associated with litter size in the first parity.”

Prevalence: "In 2001, the insertion frequency was already 0.23. Even though all homozygous boars are eliminated from the population due to infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established." (Sironen et al., 2014)

Breed: Large White, Finland (Pig) (VBO_0012408).
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
SPEF2 sperm flagellar 2 Sus scrofa 16 NC_010458.4 (21088463..21264591) SPEF2 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
392 Sperm, short tail SPEF2 splicing Naturally occurring variant 16 an inserted retrotransposon within an intron 2006 16549801

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2021). OMIA:002435-9823: 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 Derks, M.F.L., Steensma, M. :
Review: Balancing selection for deleterious alleles in livestock. Front Genet 12:761728, 2021. Pubmed reference: 34925454. DOI: 10.3389/fgene.2021.761728.
2014 Sironen, A., Fischer, D., Laiho, A., Gyenesei, A., Vilkki, J. :
A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reproductive organs. Anim Genet 45:500-7, 2014. Pubmed reference: 24712415. DOI: 10.1111/age.12153.
2012 Sironen, A., Uimari, P., Iso-Touru, T., Vilkki, J. :
L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire population. J Anim Breed Genet 129:92-7, 2012. Pubmed reference: 22394230. DOI: 10.1111/j.1439-0388.2011.00977.x.
2008 Kopp, C., Ijäs, R., Flyckt, A., Taponen, J., Parvinen, M., Andersson, M. :
Morphometric evaluations of testicular tissues from azoospermic boars in Finnish Yorkshire and Landrace breeds. Theriogenology 70:1129-35, 2008. Pubmed reference: 18640712. DOI: 10.1016/j.theriogenology.2008.06.034.
Kopp, C., Sironen, A., Ijäs, R., Taponen, J., Vilkki, J., Sukura, A., Andersson, M. :
Infertile boars with knobbed and immotile short-tail sperm defects in the Finnish Yorkshire breed. Reprod Domest Anim 43:690-5, 2008. Pubmed reference: 18397189. DOI: 10.1111/j.1439-0531.2007.00971.x.
2007 Sironen, A., Vilkki, J., Bendixen, C., Thomsen, B. :
Infertile Finnish Yorkshire boars carry a full-length LINE-1 retrotransposon within the KPL2 gene. Mol Genet Genomics 278:385-91, 2007. Pubmed reference: 17610085. DOI: 10.1007/s00438-007-0256-7.
2006 Mikkola, M., Sironen, A., Kopp, C., Taponen, J., Sukura, A., Vilkki, J., Katila, T., Andersson, M. :
Transplantation of normal boar testicular cells resulted in complete focal spermatogenesis in a boar affected by the immotile short-tail sperm defect. Reprod Domest Anim 41:124-8, 2006. Pubmed reference: 16519717. DOI: 10.1111/j.1439-0531.2006.00651.x.
Sironen, A., Thomsen, B., Andersson, M., Ahola, V., Vilkki, J. :
An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig. Proc Natl Acad Sci U S A 103:5006-11, 2006. Pubmed reference: 16549801. DOI: 10.1073/pnas.0506318103.
2002 Sironen, A.I., Andersson, M., Uimari, P., Vilkki, J. :
Mapping of an immotile short tail sperm defect in the Finnish Yorkshire on porcine Chromosome 16 Mammalian Genome 13:45-49, 2002. Pubmed reference: 11773969.
Sukura, A., Makipaa, R., Vierula, M., Rodriguez-Martinez, H., Sundback, P., Andersson, M. :
Hereditary sterilizing short-tail sperm defect in Finnish Yorkshire boars Journal of Veterinary Diagnostic Investigation 14:382-388, 2002. Pubmed reference: 12296389.
2000 Andersson, M., Peltoniemi, O.A.T., Makinen, A., Sukura, A., Rodriguez-Martinez, H. :
The hereditary 'short tail' sperm defect - A new reproductive problem in Yorkshire boars Reproduction in Domestic Animals 35:59-63, 2000.

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  • Created by Imke Tammen2 on 27 Sep 2021