Overview
Atypical hypotonia-cystinuria syndrome (also called 2p21 deletion syndrome or HCS) is a rare genetic condition caused by a deletion of genetic material on chromosome 2. This deletion removes parts of two neighboring genes — SLC3A1 and PREPL — which leads to a combination of two distinct problems in the body. First, the loss of SLC3A1 function causes cystinuria, a condition where the kidneys cannot properly reabsorb the amino acid cystine, leading to the formation of kidney stones. Second, the loss of PREPL function causes low muscle tone (hypotonia) from birth, along with feeding difficulties, growth delays, and sometimes hormonal issues. Babies with this syndrome are typically floppy at birth and have trouble feeding, which can lead to failure to thrive. As children grow, they may develop recurrent kidney stones made of cystine. Some children also experience mild developmental delays. The severity can vary depending on the exact size of the chromosomal deletion — larger deletions may remove additional genes and cause more complex symptoms. There is currently no cure for atypical hypotonia-cystinuria syndrome. Treatment focuses on managing each symptom separately. Kidney stones are managed with high fluid intake, dietary changes, and medications that help dissolve cystine. Low muscle tone is addressed through physical therapy and occupational therapy. Growth and feeding problems may require nutritional support. With proper management, many individuals can lead fulfilling lives, though lifelong monitoring is needed.
Also known as:
Key symptoms:
Low muscle tone (floppiness) from birthFeeding difficulties in infancyFailure to thrive or poor weight gainRecurrent kidney stonesDelayed motor milestones like sitting and walkingGrowth delay or short statureMild developmental delayExcessive sleepiness or fatigueObesity in later childhoodHormonal imbalances such as growth hormone deficiencyBlood in the urine from kidney stonesAbdominal or flank pain from kidney stones
Autosomal recessive
Passed on when both parents carry the same gene change; often skips generations
Neonatal
Begins at or shortly after birth (first 4 weeks)
Treatments
No FDA-approved treatments are currently listed for Atypical hypotonia-cystinuria syndrome.
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Specialists
View all specialists →No specialists are currently listed for Atypical hypotonia-cystinuria syndrome.
Treatment Centers
8 centersBaylor College of Medicine Rare Disease Center ↗
Baylor College of Medicine
📍 Houston, TX
🏥 NORDStanford Medicine Rare Disease Center ↗
Stanford Medicine
📍 Stanford, CA
🔬 UDNNIH Clinical Center Undiagnosed Diseases Program ↗
National Institutes of Health
📍 Bethesda, MD
🔬 UDNUCLA UDN Clinical Site ↗
UCLA Health
📍 Los Angeles, CA
🔬 UDNBaylor College of Medicine UDN Clinical Site ↗
Baylor College of Medicine
📍 Houston, TX
🔬 UDNHarvard/MGH UDN Clinical Site ↗
Massachusetts General Hospital
📍 Boston, MA
🏥 NORDMayo Clinic Center for Individualized Medicine ↗
Mayo Clinic
📍 Rochester, MN
👤 Mayo Clinic Center for Individualized Medicine
🏥 NORDUCLA Rare Disease Day Program ↗
UCLA Health
📍 Los Angeles, CA
Travel Grants
No travel grants are currently matched to Atypical hypotonia-cystinuria syndrome.
Community
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Caregiver Resources
NORD Caregiver Resources
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Family & Caregiver Grants
Financial assistance programs specifically for caregivers of rare disease patients.
Social Security Disability
Learn how rare disease patients may qualify for SSDI/SSI benefits.
Questions for your doctor
Bring these to your next appointment
- Q1.What is the exact size of my child's genetic deletion, and does it affect any genes beyond SLC3A1 and PREPL?,How often should my child have kidney ultrasounds to check for stones?,What is the best fluid intake goal for my child's age and weight to prevent kidney stones?,Should my child be tested for growth hormone deficiency or other hormonal issues?,What therapies (physical, occupational, speech) does my child need, and how often?,Are there any clinical trials or new research studies we should know about?,What should I do if I suspect my child is passing a kidney stone — when should we go to the emergency room?
Common questions about Atypical hypotonia-cystinuria syndrome
What is Atypical hypotonia-cystinuria syndrome?
Atypical hypotonia-cystinuria syndrome (also called 2p21 deletion syndrome or HCS) is a rare genetic condition caused by a deletion of genetic material on chromosome 2. This deletion removes parts of two neighboring genes — SLC3A1 and PREPL — which leads to a combination of two distinct problems in the body. First, the loss of SLC3A1 function causes cystinuria, a condition where the kidneys cannot properly reabsorb the amino acid cystine, leading to the formation of kidney stones. Second, the loss of PREPL function causes low muscle tone (hypotonia) from birth, along with feeding difficulties,
How is Atypical hypotonia-cystinuria syndrome inherited?
Atypical hypotonia-cystinuria syndrome follows a autosomal recessive inheritance pattern. Genetic counseling can help families understand recurrence risk and testing options.
At what age does Atypical hypotonia-cystinuria syndrome typically begin?
Typical onset of Atypical hypotonia-cystinuria syndrome is neonatal. Age of onset can vary across affected individuals.