CSNK1D rs104894561: What Your Genotype Means
The rs104894561 variant is a rare genetic change in the CSNK1D gene that alters the structure of the encoded kinase enzyme. This specific mutation is associated with Familial Advanced Sleep Phase Syndrome type 2 (FASPS2), a condition characterized by a significantly shifted circadian rhythm.
What each genotype means
Typical sleep-wake cycle
This genotype represents the common, non-variant form of the CSNK1D gene. It is not associated with the specific sleep phase shifts observed in familial advanced sleep phase syndrome type 2 (FASPS2).
This is the most common genotype found in the general population.
Advanced sleep phase tendency
This genotype, which results in a p.Thr44Ala amino acid change, is associated with Familial Advanced Sleep Phase Syndrome 2 (FASPS2). Individuals with this variant often experience a circadian rhythm shift, typically falling asleep and waking up approximately 4 hours earlier than the general population. This condition is inherited in an autosomal dominant manner.
This specific genotype is extremely rare, with an allele frequency of less than 0.0001 in large population databases like gnomAD.
Advanced sleep phase risk
While the heterozygous (A/G) state is well-documented in the literature regarding FASPS2, the homozygous (G/G) state is exceptionally rare. Research indicates that the G allele impairs kinase activity, and individuals carrying this variant should be aware of its association with early sleep-wake timing.
This genotype is exceedingly rare and is not typically observed in standard population frequency datasets.
Understanding the Variant
The variant rs104894561, often referred to as p.Thr44Ala or T44A, is a single nucleotide polymorphism (SNP) located within the CSNK1D gene on chromosome 17. In this specific genetic change, the amino acid threonine is replaced by alanine at position 44 of the protein sequence. This alteration occurs in a critical region of the enzyme, which can impact its functional efficiency. Because this variant is extremely rare in the general population, it is primarily studied in the context of specific families who exhibit distinct patterns of sleep-wake cycles. It is classified as a missense variant, meaning the change in the DNA sequence results in a different amino acid being incorporated into the protein, potentially affecting how that protein performs its biological tasks within the cell.
The Role of the CSNK1D Gene
The CSNK1D gene encodes the protein casein kinase 1 delta (CK1δ), an enzyme that plays a vital role in various cellular processes. One of its most well-documented functions is the regulation of the circadian rhythm, the internal biological clock that governs sleep-wake cycles. CK1δ acts by phosphorylating key clock proteins, such as the Period (PER) proteins. By adding phosphate groups to these proteins, CK1δ helps control their stability and their movement into the cell nucleus, which in turn dictates the timing of the circadian cycle. Beyond sleep regulation, this kinase is involved in DNA repair, apoptosis, and microtubule dynamics. Because it is a central regulator of these fundamental processes, the proper function of the CSNK1D gene is essential for maintaining the timing of many physiological activities.
Research and Clinical Associations
Research has strongly associated the rs104894561 variant with Familial Advanced Sleep Phase Syndrome type 2 (FASPS2). In individuals carrying this variant, the mutated kinase shows reduced enzymatic activity in laboratory studies. This impairment disrupts the normal phosphorylation of clock proteins, leading to a shortened circadian period. Consequently, affected individuals often experience an 'advanced' sleep phase, meaning they feel the urge to go to bed and wake up several hours earlier than the general population. While the evidence linking this specific mutation to FASPS2 is strong within affected families, it is important to note that sleep patterns are complex and influenced by many genetic and environmental factors. The presence of this variant is a specific, rare cause of sleep phase advancement and should not be considered a universal explanation for all sleep timing variations.
Population Frequency
The rs104894561 variant is extremely rare in the general population, with an allele frequency reported as less than 0.0001 in large-scale databases like gnomAD. Because it is so uncommon, it is not typically found in the general population and is usually identified through clinical investigation of families with inherited sleep disorders.
Interpreting Your Genetic Information
If you have information regarding your status for rs104894561, it is important to understand that this is a rare variant with a specific clinical association. Genetic testing results should always be interpreted in the context of your personal and family medical history. This information is for educational purposes and does not constitute a medical diagnosis. If you are concerned about your sleep patterns or believe you may have a sleep disorder, you should consult with a healthcare professional or a sleep specialist. They can provide appropriate clinical evaluations, such as sleep logs or actigraphy, to assess your circadian rhythm. Never use genetic data to make medical decisions or change your lifestyle habits without professional guidance. A clinician can help determine if your sleep patterns are related to genetic factors or other underlying health conditions.
How common is this variant?
The rs104894561 variant is extremely rare in gnomAD, with an allele frequency of less than 0.0001 across global populations.
Frequently asked questions
What is Familial Advanced Sleep Phase Syndrome type 2?
FASPS2 is a rare, inherited sleep disorder where an individual's internal clock is set to an earlier time than normal. People with this condition typically fall asleep and wake up several hours earlier than the average person.
Does having the rs104894561 variant mean I have a sleep disorder?
Not necessarily. While this variant is associated with FASPS2, genetic findings must be evaluated by a doctor alongside your actual sleep patterns and clinical history. A genetic result alone is not a diagnosis.
Can I change my sleep cycle if I have this variant?
Sleep patterns are influenced by both genetics and environment. If you are experiencing sleep difficulties, a sleep specialist can discuss behavioral strategies or other interventions that may help manage your symptoms.
Is this variant common in the general population?
No, this variant is extremely rare. It is not a common genetic change found in the general population and is primarily identified in specific families affected by advanced sleep phase syndrome.
Sources & further reading
Educational information only, last refreshed 9/19/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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This missense mutation (Thr44Ala) in the CSNK1D gene is a known cause of familial advanced sleep phase syndrome (FASPS).
The T44A missense mutation in CSNK1D accelerates circadian period length and is linked to familial advanced sleep phase syndrome and migraine.
A rare missense variant (p.His205Arg) in CSNK1D causing familial advanced sleep phase syndrome type 2.
Missense variant (Thr44Ala) in CSNK1D; pathogenic for Familial Advanced Sleep Phase Syndrome 2 (FASPS2).
Exonic variant in CSNK1D; while some variants are linked to advanced sleep-wake phase syndrome, population-wide penetrance is often low.
This variant in CSNK1D is linked to familial advanced sleep phase syndrome, influencing circadian period length.