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Neonatal intrahepatic cholestasis due to citrin deficiency is a mild subtype of citrin deficiency characterized clinically by low birth weight, failure to thrive, transient intrahepatic cholestasis, multiple aminoacidemia, galactosemia, hypoproteinemia, hepatomegaly, decreased coagulation factors, hemolytic anemia, variable but mostly mild liver dysfunction, and hypoglycemia.
Features include always present findings: Hypermethioninemia, Hyperthreoninemia, Hypertyrosinemia, and Elevated circulating alkaline phosphatase concentration and others. 23 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Lab test results | 6 | Elevated circulating alkaline phosphatase concentration, Increased serum bile acid concentration, Elevated circulating alanine aminotransferase concentration |
Digestive system | 5 | Low HDL ("good") cholesterol (decreased hdl cholesterol concentration), Liver scarring (cirrhosis) (cirrhosis), Intrahepatic cholestasis |
Growth and development | 2 | Failure to thrive, Growth delay |
Citrin deficiency has three age-dependent, variable clinical phenotypes: neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD), failure to thrive and dyslipidemia caused by citrin deficiency (FTTDCD), and citrullinemia type II (CTLN2). Citrin deficiency can manifest in newborns or infants as NICCD characterized by a diverse set of metabolic abnormalities, including citrullinemia, galactosemia, hypoglycemia, and sometimes hyperammonemia that is likely secondary to liver dysfunction. In most individuals, the clinical manifestations of NICCD improve or resolve by age 12 months. However, some individuals remain symptomatic with progression to FTTDCD, which is characterized by poor weight gain, poor linear growth, dyslipidemia, recurrent hypoglycemia, and fatigue. These individuals may have a silent remission period until after adolescence; 10%-20% evolve into the very severe or even fatal metabolic condition CTLN2, characterized by hyperammonemia, severe liver steatosis, cognitive impairment with sudden episodes of unconsciousness due to brain edema, and pancreatitis. The proportion of people with NICCD that evolve into CTLN2 is unknown. Often, FTTDCD and CTLN2 are characterized by the individual's preference for protein-rich and/or lipid-rich foods and aversion to carbohydrate-rich foods. Neonatal Intrahepatic Cholestasis Caused by Citrin Deficiency (NICCD) Table 2. Neonatal Intrahepatic Cholestasis Caused by Citrin Deficiency: Frequency of Select Features
Clinical Feature/ Laboratory Analyte | Proportion of Persons w/Feature1 | Comment |
|---|---|---|
Liver disease | Cholestasis | 79% |
SLC25A13 function has not been fully characterized.
Neonatal intrahepatic cholestasis due to citrin deficiency is associated with mutations in the SLC25A13 gene on chromosome 7.
No clinically relevant genotype-phenotype correlations are known for this disorder.
Source: GeneReviews — "Citrin Deficiency"
Notably, the penetrance is not 100% for citrin deficiency as an autosomal recessive condition. In addition, there appears to be a difference in penetrance of the CTLN2 phenotype related to the sex of the individual.
Of 418 individuals with biallelic SLC25A13 pathogenic variants, seven individuals had no clinical manifestations, indicating a penetrance of 98.3% .
The male-to-female ratio in individuals with NICCD is roughly equal (73:80), while the male-to-female ratio in individuals with CTLN2 is 2.4 to 1 (120:50) . The unequal male-to-female ratio in CTLN2 suggests that for unknown reasons, among individuals with biallelic SLC25A13 pathogenic variants, females are more resistant to the CTLN2 phenotype than males.
Source: GeneReviews — "Citrin Deficiency"
Citrin deficiency has three clinical phenotypes: neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD), failure to thrive and dyslipidemia caused by citrin deficiency (FTTDCD), and citrullinemia type II (CTLN2) . A symptomatic individual may have either untreated NICCD due to newborn screening (NBS) not performed, false negative NBS result, caregivers not adherent to recommended treatment following a positive NBS result, or manifestations associated with later-onset citrin deficiency (FTTDCD or CTLN2).
Suggestive Findings
Abnormal NBS result. NBS for citrin deficiency is primarily based on quantification of the analyte citrulline on dried blood spots. Note: Dried blood spots also show elevated galactose, ...
Source: GeneReviews — "Citrin Deficiency"
Increased plasma concentration of citrulline is also present in citrullinemia type 1, argininosuccinate lyase deficiency, pyruvate carboxylase deficiency, and lysinuric protein intolerance . Hyperammonemia also occurs in urea cycle disorders, which result from defects in the metabolism of the nitrogen produced by the breakdown of protein and other nitrogen-containing molecules (see Urea Cycle Disorders Overview). Severe deficiency or total absence of activity of any of the first four enzymes in the pathway (CPSI, OTC, ASS1, ASL) or the cofactor producer (NAGS) results in the accumulation of ammonia and other precursor metabolites during the first few days of life in most affected individuals.
Source: GeneReviews — "Citrin Deficiency"
Genetic testing for SLC25A13 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for neonatal intrahepatic cholestasis due to citrin deficiency has been reported in the published literature.
No approved treatments are currently available for neonatal intrahepatic cholestasis due to citrin deficiency. The disease remains an area of unmet medical need.
Although progress has been made [, , , ], no well-recognized clinical practice guidelines for citrin deficiency have been published. The following recommendations are based on the authors' personal experience managing large cohorts of individuals with this disorder over a long period of time.
To establish the extent of disease and needs in an individual diagnosed with citrin deficiency, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended.
Table 5.
Citrin Deficiency: Recommended Evaluations Following Initial Diagnosis by Phenotype
Evaluation | Phenotype
NICCD | FTTDCD | CTLN2
Consultation w/metabolic physician/ biochemical geneticist specialist metabolic dietitian1 | • Transfer to specialist center w/experience in mgmt of inherited metabolic diseases (strongly recommended).
Plasma amino acid analysis to measure citrulline other amino acids
Consider short hospitalization at a center of expertise for inherited metabolic conditions to provide caregivers w/detailed education (natural history, maintenance emergency treatment, prognosis).
| Referral to specialist center w/experience in mgmt of inherited metabolic diseases; includes plasma amino acid analysis
| Perform detailed anthropometric exam eval using age- sex-matched growth standards. | Assess weight.
Investigate feeding pattern. | Investigate carbohydrate, protein, lipid composition of diet.
Source: GeneReviews — "Citrin Deficiency"
Low-protein/high-caloric (high-carbohydrate) diet. Although a low-protein/high-caloric diet helps prevent hyperammonemia in urea cycle enzyme deficiencies, it is harmful for individuals with all forms of citrin deficiency (i.e., neonatal intrahepatic cholestasis caused by citrin deficiency [NICCD)], failure to thrive and dyslipidemia caused by citrin deficiency [FTTDCD], or citrullinemia type II [CTLN2]) [, , , ]. A high-carbohydrate diet may increase nicotinamide adenine dinucleotide hydrogen (NADH) production, disturb urea synthesis, and stimulate the citrate-malate shuttle, resulting in hyperammonemia, fatty liver, and hypertriglyceridemia [, , , ]. Infusion of sugars including glycerol, fructose, and glucose. Severe brain edema treated with glycerol-containing osmotic agents has resulted in continued deterioration and is contraindicated in those with CTLN2 . Degradation of large amounts of glycerol and fructose generates NADH in liver cytosol, which may disturb liver function . Infusion of high-concentration glucose may also exacerbate hyperammonemia . Mannitol infusion appears to be safer . Alcohol. Drinking alcohol can trigger the onset of CTLN2 because alcohol dehydrogenase generates NADH in the cytosol of the liver.
Source: GeneReviews — "Citrin Deficiency"
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "Citrin Deficiency"
3 trials found
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. Table 7. Citrin Deficiency: Recommended Surveillance
System/Concern | Evaluation | Frequency/Comment |
|---|---|---|
Metabolic balance/ Nutrition | Eval by an experienced metabolic physician metabolic nutritionist; may include assessments of biochemical /or metabolome analytes (incl plasma amino acids) w/adjustments in medication dietary therapies based on age, weight, diet | As recommended by metabolic center Education of parents caregivers such that diligent observation mgmt can be administered expediently in setting of intercurrent illness or other catabolic stressors |
Growth | Assess height, weight, head circumference. | At each visit throughout childhood adolescence; continue weight assessment at each visit throughout adulthood |
Liver function | ALT, AST, albumin, -GTP, ALP, bilirubin, bile acids, cholesterol, triglyceride, AFP, coagulation, ammonia to assess liver function | As clinically indicated Pancreatic function |
Development/Behavior | Monitor developmental milestones. | At each visit throughout childhood adolescence; Neuropsychological testing using age-appropriate standardized assessment batteries; Standardized quality-of-life assessment tools for affected persons parents/caregivers |
Anemia | Complete blood count, ferritin level | As clinically indicated AFP = alpha-fetoprotein; ALP = alkaline phosphatase; ALT = alanine transaminase; AST = aspartate transaminase; PSTI = pancreatic secretory trypsin inhibitor; US = ultrasound; -GTP = gamma-glutamyl transpeptidase 1. |
Source: GeneReviews — "Citrin Deficiency"
Phenotype severity distribution: 16 always present features.
Estimated prevalence: Unknown (Unknown prevalence).
3 clinical trials registered. Interventions under study include other interventions and drug therapy. Pipeline includes 1 PHASE1, 1 NA. Research is sponsored by a mix of industry and academic institutions.
22 publications have been identified in PubMed for neonatal intrahepatic cholestasis due to citrin deficiency. Research spans Diagnostic / Biomarker (27%), Review / Meta-Analysis (27%), and Epidemiology / Natural History (18%).
Research Type | Count | % of Total |
|---|---|---|
Testing and diagnosis research | 6 | 27% |
Research summaries | 6 | 27% |
Disease patterns and progression | 4 | 18% |
Patient case studies | 3 | 14% |
Other research | 2 | 9% |
Laboratory research | 1 | 5% |
Kido J (2026). [PMID: 41923674](https://pubmed.ncbi.nlm.nih.gov/41923674/). *Mol Genet Metab*. [Diagnostic / Biomarker]
Chen L (2026). [PMID: 42106161](https://pubmed.ncbi.nlm.nih.gov/42106161/). *J Pediatr (Rio J)*. [Epidemiology / Natural History]
Kido J (2025). [PMID: 40309478](https://pubmed.ncbi.nlm.nih.gov/40309478/). *Hum Mutat*. [Review / Meta-Analysis]
Zou Y (2025). [PMID: 40665261](https://pubmed.ncbi.nlm.nih.gov/40665261/). *BMC Gastroenterol*. [Case Report / Case Series]
Wang P (2025). [PMID: 39799340](https://pubmed.ncbi.nlm.nih.gov/39799340/). *Orphanet J Rare Dis*. [Diagnostic / Biomarker]
Wang P (2025). [PMID: 41063287](https://pubmed.ncbi.nlm.nih.gov/41063287/). *Orphanet J Rare Dis*. [Diagnostic / Biomarker]
Yeo M (2025). [PMID: 40780027](https://pubmed.ncbi.nlm.nih.gov/40780027/). *Mol Genet Metab*. [Epidemiology / Natural History]
Ghosh U (2025). [PMID: 40893336](https://pubmed.ncbi.nlm.nih.gov/40893336/). *J Clin Exp Hepatol*. [Other]
Lacabanne D (2025). [PMID: 40145619](https://pubmed.ncbi.nlm.nih.gov/40145619/). *J Inherit Metab Dis*. [Review / Meta-Analysis]
Kido J (2025). [PMID: 40840052](https://pubmed.ncbi.nlm.nih.gov/40840052/). *Mol Genet Metab*. [Epidemiology / Natural History]
Data assembled from 8 of 12 sources · Last updated Sep 20, 2026, 5:34 PM UTC
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71% |
— |
Hypoproteinemia | 39% | — |
Prolonged prothrombin time | 34% | — |
Fatty liver | 33% | Liver histology includes cholestasis, diffuse macrovesicular microvesicular steatosis, inflammatory infiltration, fibrosis |
Hyperlipidemia | 24% | — |
Hepatomegaly | 22% | — |
Hyperammonemia | 11% | Ammonia 100 umol/L |
Growth impairment (poor weight gain) | 32% | Usually small for gestational age; growth failure until age 6-9 mos |
Hypoglycemia | 30% | — |
Amino acid profile | citrulline (~80%) | Also elevated threonine, methionine, arginine, tyrosine |
Anemia | 17% | — |
Seizures | 5% | 1. Liver dysfunction. Children younger than age one year with NICCD have intrahepatic cholestasis. |
Source: GeneReviews — "Citrin Deficiency"