OMIA 000042-9031 : Analphalipoproteinaemia in Gallus gallus
Category: Homeostasis / metabolism phene
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Z-linked recessive
Considered a defect: yes
Key variant known: yes
Year key variant first reported: 2002
Species-specific name: Wisconsin hypoalpha mutant (WHAM)
Mapping: Bitgood (1985) and Bitgood (1988) reported loose linkage of the WHAM locus to loci B and ID on the chicken Z chromosome. Fridolfsson et al. (1998) showed that this region contains the genes ALDOB and MUSK, which were physically mapped to Zq1.5-1.6, which is homologous with human HSA9q22.3–q32.
Molecular basis: The causal mutation for this disorder was identified via a comparative positional cloning approach (as described in the Mapping section above, the locus was mapped to a region of the chicken Z chromosome (GGAZ) that is homologous to human HSA9q22.3-32, which includes the gene ABCA1, mutations in which cause Tangier disease, which is similar to this chicken disorder). Sequencing of the chicken ABCA1 gene by Attie et al. (2002) revealed the causal mutation as "a missense mutation [G265A] near the N-terminus of the protein (E89K)". The authors reported that "This alteration is a non-conservative amino acid substitution at a residue that is conserved in the ABCA1 gene between human, mouse, chicken, and Takifugu rubripes (“fugu”)".
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|ABCA1||ATP-binding cassette, sub-family A (ABC1), member 1||Gallus gallus||Z||NC_052572.1 (55505344..55410930)||ABCA1||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||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|2||Wisconsin hypoalpha mutant (WHAM), United States of America (Chicken)||Analphalipoproteinaemia||ABCA1||missense||Naturally occurring variant||GRCg6a||Z||g.54877918C>T||c.265G>A||p.(E89K)||2002||12364545||Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool|
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.
|2002||Attie, A.D., Hamon, Y., Brooks-Wilson, A.R., Gray-Keller, M.P., MacDonald, M.L.E., Rigot, V., Tebon, A., Zhang, L.H., Mulligan, J.D., Singaraja, R.R., Bitgood, J.J., Cook, M.E., Kastelein, J.J.P., Chimini, G., Hayden, M.R. :>|
|Identification and functional analysis of a naturally occurring E89K mutation in the ABCA1 gene of the WHAM chicken Journal of Lipid Research 43:1610-1617, 2002. Pubmed reference: 12364545.|
|1998||Fridolfsson, A.K., Cheng, H., Copeland, N.G., Jenkins, N.A., Liu, H.C., Raudsepp, T., Woodage, T., Chowdhary, B., Halverson, J., Ellegren, H. :>|
|Evolution of the avian sex chromosomes from an ancestral pair of autosomes. Proc Natl Acad Sci U S A 95:8147-52, 1998. Pubmed reference: 9653155.|
|1992||Poernama, F., Subramanian, R., Cook, M.E., Attie, A.D. :>|
|High Density Lipoprotein Deficiency Syndrome in Chickens Is Not Associated with an Increased Susceptibility to Atherosclerosis Arteriosclerosis and Thrombosis 12:601-607, 1992. Pubmed reference: 1576121.|
|1990||Poernama, F., Schreyer, S.A., Bitgood, J.J., Cook, M.E., Attie, A.D. :>|
|Spontaneous High Density Lipoprotein Deficiency Syndrome Associated with a Z-Linked Mutation in Chickens Journal of Lipid Research 31:955-963, 1990. Pubmed reference: 2373963.|
|1988||Bitgood, J.J. :>|
|Linear relationship of the loci for barring, dermal melanin inhibitor, and recessive white skin on the chicken Z chromosome Poultry Science 67:530–533, 1988.|
|1985||Bitgood, J.J. :>|
|Additional linkage relationships within the Z chromosome of the chicken Poultry Science 64:2234–2238, 1985.|
- Created by Frank Nicholas on 15 Nov 2005
- Changed by Frank Nicholas on 09 Dec 2011
- Changed by Frank Nicholas on 21 Sep 2012