- Splenomegaly (HP:0001744): Abnormal increased size of the spleen. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
- Autoimmune hemolytic anemia (HP:0001890): An autoimmune form of hemolytic anemia. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:231154)
- Autoimmune neutropenia (HP:0001904): Abnormal decrease of the absolute number of neutrophils in the blood, per microlitre, compared to a reference range for a given sex and age-group, accompanied by the detection of anti-neutrophil antibodies. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:231154)
- Immunodeficiency (HP:0002721): Failure of the immune system to protect the body adequately from infection, due to the absence or insufficiency of some component process or substance. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
- Autoimmunity (HP:0002960): The occurrence of an immune reaction against the organism's own cells or tissues. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:231154)
- Severe combined immunodeficiency (HP:0004430): A type of primary immune deficiency that is characterized by a more severe defect in both the T- and B-lymphocyte systems. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
- Decreased total T cell count (HP:0005403): Abnormal decrease in the absolute number of T cells, commonly characterized as CD3+ lymphocytes, per microliter of blood, compared to a reference range for a given sex and age-group. These may include both TCR alpha/beta and gamma/delta T cells. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
- Interstitial pneumonitis (HP:0006515). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
- Decreased total B cell count (HP:0010976): The absolute number of B cells in the blood, per microlitre is below the lower limit of normal of the reference range for the appropriate sex and age-group. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
- Sepsis (HP:0100806): Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:231154)
These phenotypes are associated with the disease Combined immunodeficiency due to partial RAG1 deficiency (ORPHA:231154).