Primary carnitine deficiency is an autosomal recessive disorder caused by loss-of-function variants in the SLC22A5 gene, which sits on chromosome 5q31.1 and encodes a protein called organic cation transporter 2, or OCTN2. This transporter is the gatekeeper of carnitine homeostasis: it pumps carnitine into cells across the plasma membrane and reabsorbs it in the renal proximal tubules, maintaining intracellular free carnitine concentrations 20 to 50 times higher than those outside the cell. When both copies of the gene are disabled, carnitine floods out of the body in urine and cells are starved of a molecule they desperately need to import long-chain fatty acids into mitochondria for beta-oxidation, the metabolic pathway that supplies energy during fasting and prolonged exertion.

The clinical consequences are stark. Roughly half of affected children develop hypoketotic hypoglycemia between 3 months and 2 years of age, a dangerous combination of low blood sugar and absent ketone bodies that can spiral into hepatic encephalopathy, lethargy, and hyperammonemia. The other half present between 2 and 4 years old with skeletal muscle weakness, poor exercise tolerance, cardiomyopathy, and arrhythmias. In severe cases, sudden death can occur, and multiple unexplained deaths among young adults in the Faroe Islands, where the disorder affects as many as 1 in 297 people, have been attributed to untreated primary carnitine deficiency. Yet the condition is also one of the most treatable inherited metabolic disorders known: early diagnosis and oral L-carnitine supplementation, typically at 50 to 100 milligrams per kilogram per day, can prevent irreversible damage entirely.

The screening pipeline described in the study relies on tandem mass spectrometry, or MS/MS, to measure free carnitine, abbreviated C0, in dried blood spots collected from newborns within 3 days of birth. Following Chinese expert consensus, the team used a cutoff of 10 micromoles per liter. Of the 439,486 newborns screened over ten years, 1,518, or 0.35 percent, fell below that threshold on the initial test. Nearly all of them, 1,517 infants, were recalled for re-screening, and 154 showed persistently low C0 levels. Of the 152 who completed full diagnostic evaluation, 20 received a clinically relevant diagnosis, a diagnostic yield of 13.16 percent. Seventeen were diagnosed with primary carnitine deficiency, yielding a screening-detected prevalence in Yancheng of 1 in 25,852, while three cases traced back to maternal carnitine deficiency transmitted through the placenta rather than an inherited defect in the infant.

The numbers reveal the central challenge of screening for this disease. Carnitine crosses the placenta freely during pregnancy, and neonatal levels are strongly shaped by maternal factors, so a normal mother can partially buffer a genuinely affected newborn, keeping the infant’s C0 above the minimum value on day 3. Physiological carnitine decline during pregnancy, premature sample collection, insufficient intake from exclusive breastfeeding, prematurity, low birth weight, and cesarean section all inflate the false-positive rate. The statistical analysis made this tension visible: the PCD group’s median C0 fell from 7.33 micromoles per liter at initial screening to 4.98 at re-screening, a significant drop, while the false-positive group’s median barely moved from 8.45 to 8.22, a non-significant change. The maternal deficiency group, unusually, rose from 4.33 to 4.98. But the ranges overlapped across all three groups, which means C0 measurements alone cannot settle a diagnosis.

That is where genetics entered the picture. The team sequenced the exons and flanking intronic regions of SLC22A5 in recalled newborns using the DNBSEQ-T7 platform at an average depth of at least 200-fold, then validated every variant by Sanger sequencing and classified pathogenicity under American College of Medical Genetics and Genomics guidelines. Fifteen of the 17 PCD infants carried two pathogenic variants, four of them homozygous, giving molecular confirmation of the biochemical picture. Across these patients, 32 variants spanning 10 distinct sites were identified, all in exonic regions, and missense changes dominated. One variant stood out: c.1400C>G, which swaps a serine for a cysteine at position 467 of the OCTN2 protein, accounted for 13 of the 32 variants, or 40.63 percent, making it the clear hotspot in this region of Jiangsu Province.

The hotspot finding carries real practical weight, because SLC22A5 variant spectra differ sharply across ethnic groups and regions. The common variant in Italy is c.505C>T; in the United States it is c.136C>T; and c.1400C>G ranks among the most frequent in Japan and has not been reported in non-East Asian populations. Large-scale Chinese studies have flagged c.1400C>G, c.51C>G, and c.760C>T as common, but with regional variation. In Yancheng, c.1400C>G towered over the second most frequent variant, c.51C>G at 21.88 percent, while c.760C>T appeared only once. Knowing which variants dominate locally allows laboratories to build faster, cheaper targeted molecular probes rather than sequencing the entire gene for every recalled infant.

The study also confronted the limits of genetic testing head-on. Two of the 17 PCD infants carried only one detectable variant, yet their C0 levels stayed below 10 micromoles per liter across three consecutive measurements with adequate feeding, their mothers had normal carnitine levels, and no secondary cause could be found, supporting a clinical diagnosis of PCD. This is not unusual: sequencing that covers only coding regions and 10 base pairs of flanking intronic sequence cannot detect variants in regulatory or deep intronic regions, nor methylation changes. Previous research found pathogenic variants in only 84 percent of alleles among people with impaired fibroblast carnitine transport, and in one large series only 56.4 percent of suspected PCD individuals carried biallelic variants. The authors therefore insist that diagnosis must rest on combined biochemical and genetic evaluation rather than either alone.

Follow-up, ranging from 18 months to 10 years, showed the payoff of early detection. None of the diagnosed children experienced acute metabolic decompensation, and all but one showed normal intellectual, motor, and growth development; the exception had poor exercise tolerance. Four families chose not to medicate their asymptomatic children but committed to avoiding fasting, infection, and prolonged strenuous exercise, the classic triggers of metabolic crisis. Among the three maternal deficiency cases, two mothers were themselves found to carry the c.1400C>G variant in homozygous form and were diagnosed with PCD, underscoring how newborn screening can cascade into diagnoses in asymptomatic adults who remain at risk of sudden cardiac death.

Perhaps the most forward-looking result came from a single recurrence-risk family. Their previous child carried two heterozygous SLC22A5 variants, c.865C>T, a premature stop codon, and c.1400C>G, inherited from the mother and father respectively. Sanger sequencing of amniotic fluid DNA in the next pregnancy revealed only the maternal variant, meaning the fetus had an extremely low probability of disease given the autosomal recessive inheritance and the parents’ normal phenotypes. The couple continued the pregnancy, and the newborn’s screening C0 fell within the normal range with normal follow-up. The authors are careful to frame this as a case illustration rather than general evidence, but it demonstrates that SLC22A5 testing can anchor prenatal diagnosis and informed reproductive counseling for families who already know the fear of this disease, offering certainty at a moment when it matters most.

Subject of Research: Newborn screening and prenatal genetic diagnosis of primary carnitine deficiency caused by SLC22A5 variants

Article Title: Newborn Screening of Primary Carnitine Deficiency and Prenatal Genetic Diagnosis for a Recurrence‐Risk Family

Article References: Sun, H., Zheng, J., Zhou, C., Chen, H., Zhang, L., Li, X., Bao, D., Yang, F., & Liu, J. (2026). Newborn Screening of Primary Carnitine Deficiency and Prenatal Genetic Diagnosis for a Recurrence‐Risk Family. Molecular Genetics & Genomic Medicine, 14(10), Article e70316. https://doi.org/10.1002/mgg3.70316

Image Credits: AI Generated

DOI: 10.1002/mgg3.70316

Keywords: primary carnitine deficiency, newborn screening, SLC22A5, OCTN2, tandem mass spectrometry, prenatal diagnosis, genetic testing, carnitine transporter, hypoketotic hypoglycemia, L-carnitine supplementation, autosomal recessive inheritance, China