Categories: Homeostasis / metabolism phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 261100 (trait) , 602997 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Disease-related: yes

Key variant known: yes

Year key variant first reported: 2013

Cross-species summary: Imerslund-Gräsbeck syndrome (I-GS); selective cobalamin malabsorption; megaloblastic anemia 1 (MGA1)

Species-specific description: Intestinal cobalamin malabsorption is a metabolic disorder characterized by failure to thrive, neutropenia, decreased serum cobalamin (Cbl), and nonregenerative anemia. Other signs include chronic inappetance, megaloblastic changes of the bone marrow, methylmalonic aciduria, and homocysteinemia. This phenotype can be caused by either mutations in the AMN or CUBN genes (locus heterogeneity). Adapted from the corresponding entry by John Fyfe in [OMIA 000565-9615].

History: The phenotype can be caused by either mutations in the AMN gene [OMIA 000565-9615] or the CUBN gene [this entry]. He et al (2003 & 2005) mapped and identified two independent AMN mutations in Australian Shepherds and Giant Schnauzers [OMIA 000565-9615]. More recently, Owczarek-Lipska et al. (2013) identified a frameshift mutation in the CUBN gene as cause for inestinal cobalamin malabsorption in the Border Collie.

Mapping: Intestinal cobalamin malabsorption in Border Collies was mapped to CFA 2 in a genome wide association study (GWAS) using 7 cases and 7 controls. The best raw p-value in this analysis was 4.6E-6. The critical interval was defined by homozygosity mapping and spanned 3.53 Mb (Owczarek-Lipska et al. 2013). Fyfe et al. (2013) conducted a genome scan on 19 Border Collies from families segregating for the disorder, using the Illumina 170K SNP chip. Homozygosity mapping highlighted a region on chromosome CFA2 centering on the CUBN gene.

Molecular basis: Whole genome re-sequencing of one affected Border Collie revealed 17 non-synonymous variants in the critical interval. Two of these variants were perfectly associated with intestinal cobalamin malabsorption in Border Collies. Based on the known functions of the corresponding genes the CUBN:c.8392delC frameshift variant is most likely causative for intestinal cobalamin malabsorption in Border Collies. This variant causes a premature stop codon in the open reading frame of cubilin (p.Gln2798Argfs*3) and is predicted to represent a complete loss of function allele (Owczarek-Lipska et al. 2013). CUBN and AMN form a transmembrane protein complex termed "cubam", which is essential in the uptake of cobalamin from the intestinal lumen. A defect in one of these two proteins therefore leads to intestinal cobalamin malabsorption. Other independent mutations in either the CUBN or the AMN gene very likely are responsible for this phenotype in other dog breeds. By sequencing CUBN as a very strong positional candidate gene (see Mapping section), Fyfe et al. (2013) identified the same mutation (c.8392delC; p. Gln2798Argfs*3) in their Border Collie families. Erles et al. (2018) reported "Systemic Scedosporium prolificans infection in an 11-month-old Border collie with cobalamin deficiency secondary to selective cobalamin malabsorption" due to homozygosity for the c.8392delC variant. By comparing sequence of the two candidate genes (AMN and CUBN) from the CanFam 3.1 reference genome assembly with sequence of the same two genes from the 15x whole-genome sequencing (WGS) of an affected Beagle, Drögemüller et al. (2014) identified "a single-base-pair deletion at Chr2:19,796,293 compared with the CanFam 3.1 reference genome assembly . . . . The variant lies within exon 8 of the CUBN gene and represents a frameshift mutation leading to an early premature stop codon (c.786delC). The predicted protein from the mutant allele contains <10% of the amino acids from the wild-type CUBN (p.Asp262Glufs*47). Thus, the identified variant most likely represents a complete loss-of-function allele." Fyfe et al. (2014) reported the same c.786delC mutation in affected Beagles, as did Kook et al. (2014; J Vet Intern Med and J Small Anim Pract) in a single affected Beagle. Fyfe et al. (2018): "Whole genome sequencing of two affected Komondor dogs of unknown relatedness and one parent and a clinically-normal littermate of an affected dog revealed a pathogenic single-base change in the CUBN intron 55 splice donor consensus sequence (NM_001003148.1: c.8746 + 1G > A) that was homozygous in affected dogs and heterozygous in the unaffected parents. Alleles of the variant co-segregated with alleles of the disease locus in the entire family and all more distantly-related sporadic cases. . . . This variant obliterates a splice donor consensus sequence in intron 55, predicting an abnormal RNA splicing pattern, and was thereby considered pathogenic. We confirmed the variant in all 6 affected Komondors by Sanger sequencing". Sancho et al. (2020) reported a most interesting example of an affected Beagle crossbred dog that turned out to be a compound heterozygote of the Beagle likely causal variant (c.786delC) and the Border Collie likely causal variant (c.8392delC). In other words, a genotype comprising these two deleterious variants resulted in similar clinical signs to homozygosity for either variant.

Clinical features: Signs begin around 6 to 12 weeks of age, and include failure to thrive and chronic inappetance. Affected animals also demonstrate neutropenia with hypersegmentation, nonregenerative anemia with anisocytosis and poikilocytosis, megaloblastic changes of the bone marrow, decreased serum Cbl concentrations, methylmalonic aciduria, and homocysteinemia. These animals have normal renal function, but low-molecular weight urinary protein excretion (Fyfe et al., 1991).

Pathology: In normal dogs, Cbl is ingested in the diet and binds to intrinsic factor, a glycoprotein made by the gastric mucosa and the pancreatic duct epithelium. The complex of intrinsic factor (IF) and Cbl is absorbed through binding receptors on enterocytes in the distal jejunum and ileum. Signs of intestinal cobalamin malabsorption are due to absence of receptors for the IF-Cbl complex at the brush border (Fyfe et al., 1991). Dogs are born with cobalamin stores, but they are rapidly used up during postnatal growth unless replaced from the diet. This is when signs become apparent (Fyfe et al., 1991).

Prevalence: At the time of mutation discovery Owczarek-Lipska et al. (2013) estimated the carrier frequency of the CUBN:c.8392delC defect at 6% in a cohort of 203 European Border Collies. Drögemüller et al. (2014) estimated the carrier frequency of the Beagle mutation (c.786delC) to be 9%. Mizukami et al. (2016) reported the frequency of the c.8392delC allele as 0.015 in 500 Border collies in Japan. Fyfe et al. (2018): "A population study using a simple allele-specific DNA test indicated mutant allele frequencies of 8.3 and 4.5% among North American and Hungarian Komondors, respectively."

Genetic testing: Genetic testing for the causative mutation is available. Genetic testing is recommended to confirm the clinical diagnosis in suspected cases. Genetic testing is also recommended for breeding animals to avoid the accidental mating of two carriers, which might lead to affected offspring.

Breeds: Beagle (Dog) (VBO_0200131), Border Collie (Dog) (VBO_0200193), Komondor (Dog) (VBO_0200779).
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: