Summary
Clinical characteristics.
KIF1A-related neurodevelopmental disorder (KIF1A-NDD) is both a developmental and degenerative condition with a broad phenotypic spectrum commonly including developmental delay, communication difficulties, optic nerve atrophy, seizures, progressive spastic paraplegia, peripheral and autonomic neuropathy, poor weight gain, and neurobehavioral issues including autism spectrum disorder. Manifestations most commonly appear in early childhood but may be detected as early as the neonatal period. There is significant phenotypic heterogeneity.
Management.
Supportive treatment: Multidisciplinary care by specialists in education of children with developmental delay / intellectual disability; management of seizures and pain associated with peripheral neuropathy by neurologist; management by orthopedist, physical medicine and rehabilitation specialist, or occupational therapist for fine motor development; physical therapy including stretching to help avoid contractures and falls; feeding therapy to manage dysphagia; treatment by ophthalmologist to manage refractive errors; speech-language therapy to improve communication.
Surveillance: To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, regularly scheduled evaluations by treating clinicians are recommended.
Genetic counseling.
KIF1A-NDD can be inherited in an autosomal dominant or, less commonly, autosomal recessive manner.
Autosomal dominant inheritance: Most individuals diagnosed with autosomal dominant KIF1A-NDD have the disorder as the result of a de novo pathogenic variant. Some individuals diagnosed with KIF1A-NDD have an affected parent. If a parent of the proband is affected and/or is known to have the pathogenic variant identified in the proband, the risk to the sibs of inheriting the pathogenic variant is 50%. If the KIF1A pathogenic variant identified in the proband cannot be detected in the leukocyte DNA of either parent, the recurrence risk to sibs is estimated to be 1% because of the possibility of parental gonadal mosaicism.
Autosomal recessive inheritance: If both parents are known to be heterozygous for a KIF1A pathogenic variant, each sib of an affected individual has at conception a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Carrier testing for at-risk relatives requires prior identification of the KIF1A pathogenic variants in the family.
Once the KIF1A pathogenic variant(s) have been identified in an affected family member, prenatal and preimplantation genetic testing are possible.
Diagnosis
No consensus clinical diagnostic criteria for KIF1A-related neurodevelopmental disorder (KIF1A-NDD) have been published.
Suggestive Findings
KIF1A-NDD should be considered in probands with the following clinical and brain MRI findings and family history.
Clinical findings
Brain MRI findings
Family history. Because KIF1A-NDD is typically caused by a de novo pathogenic variant, most probands represent a simplex case (i.e., a single occurrence in a family). Rarely, the family history may suggest autosomal dominant inheritance (e.g., affected males and females in multiple generations) or autosomal recessive inheritance (e.g., affected sibs and/or parental consanguinity).
Establishing the Diagnosis
The diagnosis of KIF1A-NDD is established in a proband with suggestive findings and a heterozygous pathogenic (or likely pathogenic) variant or biallelic pathogenic (or likely pathogenic) variants in KIF1A identified by molecular genetic testing (see Table 1) [Boyle et al 2021, Sudnawa et al 2024].
Note: (1) Per American College of Medical Genetics and Genomics / Association for Molecular Pathology variant interpretation guidelines, the terms "pathogenic variant" and "likely pathogenic variant" are synonymous in a clinical setting, meaning that both are considered diagnostic and can be used for clinical decision making [Richards et al 2015]. Reference to "pathogenic variants" in this GeneReview is understood to include likely pathogenic variants. (2) Identification of a KIF1A variant of uncertain significance does not establish or rule out the diagnosis.
Molecular genetic testing in a child with developmental delay or an older individual with intellectual disability may begin with exome sequencing / genome sequencing [Manickam et al 2021, van der Sanden et al 2023]. Other options include use of a multigene panel.
Note: Single-gene testing (sequence analysis of KIF1A, followed by gene-targeted deletion/duplication analysis) is rarely useful and typically NOT recommended.
Comprehensive genomic testing does not require the clinician to determine which
gene(s) are likely involved.
Exome sequencing is most commonly used, and yields results similar to an intellectual disability
multigene panel, with the additional advantage that
exome sequencing includes genes recently identified as causing intellectual disability, whereas some multigene panels may not. To date, the majority of
KIF1A pathogenic variants reported are within the
coding region and are likely to be identified on exome sequencing.
Genome sequencing is also possible.
For an introduction to comprehensive
genomic testing click
here. More detailed information for clinicians ordering genomic testing can be found
here.
A multigene panel that includes
KIF1A and other genes of interest (see
Differential Diagnosis) is most likely to identify the genetic cause of the condition in a person with a nondiagnostic
chromosome microarray while limiting identification of pathogenic variants and variants of
uncertain significance in genes that do not explain the underlying
phenotype. Note: (1) The genes included in the panel and the diagnostic
sensitivity of the testing used for each
gene vary by laboratory and are likely to change over time. (2) Some multigene panels may include genes not associated with the condition discussed in this
GeneReview. (3) In some laboratories, panel options may include a custom laboratory-designed panel and/or custom phenotype-focused
exome analysis that includes genes specified by the clinician. (4) Methods used in a panel may include
sequence analysis,
deletion/duplication analysis, and/or other non-sequencing-based tests.
For an introduction to multigene panels click
here. More detailed information for clinicians ordering genetic tests can be found
here.
Clinical Characteristics
Clinical Description
KIF1A-related neurodevelopmental disorder (KIF1A-NDD) is a developmental and degenerative condition with a broad phenotypic spectrum commonly including developmental delay, progressive spastic paraplegia, peripheral and autonomic neuropathy, autism spectrum disorder, and optic nerve atrophy [Boyle et al 2021]. There is significant phenotypic heterogeneity. Manifestations most commonly appear in early childhood but may be detected as early as the neonatal period.
To date, about 300 individuals with KIF1A-NDD have been identified [Nemani et al 2020, Pennings et al 2020, Boyle et al 2021, Nicita et al 2021, Vecchia et al 2022, Paprocka et al 2023, Sudnawa et al 2024]. The following description of the phenotypic features associated with KIF1A-NDD is based on these reports.
Developmental delay / intellectual disability
Some form of developmental delay is observed in more than 90% of individuals
Regression and cognitive decline are common, especially in those with epilepsy; however, the age of onset of regression and the rate of decline vary.
Speech and language issues
Infant feeding difficulties are common. While most individuals can eat by mouth, some require placement of a gastrostomy tube, typically due to problems with aspiration.
Neurobehavioral/psychiatric manifestations
Manifestations of sleep difficulties are seen in ~45% of individuals. These can include atypical sleep-wake cycles, difficulties falling asleep, frequent awakening during the night, and individuals who go for more than 24 hours without sleeping.
Common challenging behaviors can include stereotypies, repetitive behaviors, aggressive behaviors, and self-injurious behaviors.
Autism spectrum disorder is observed in ~25% of individuals.
Attention-deficit/hyperactivity disorder is observed in ~25% of individuals, though many have issues with hyperactivity even in the absence of this diagnosis.
Anxiety and obsessive-compulsive disorder are the most common psychiatric comorbidities.
Depression, bipolar disorder, and psychosis are common, especially starting in adolescence and adulthood.
Motor impairment and neurologic features
Hypotonia is seen in ~86% of individuals. It is often the first presenting manifestation, typically occurring in the first year of life.
Hypertonia/spasticity, seen in ~80% of individuals, often co-occur with hypotonia. Frequently, truncal hypotonia is accompanied by lower extremity hypertonia.
Excessive clumsiness / coordination disorder is reported in ~60% of individuals.
Hyperkinetic movement disorder (e.g., stereotypic movements and tics) is reported in ~20% of individuals.
Ataxia, in 28% of individuals, is associated with increased falls and injuries.
Tremors, in 22% of individuals, can limit fine motor function.
Dystonia, in 15% of individuals, can result in pain or instability.
Peripheral neuropathy, reported in ~30% of individuals, is likely underestimated. Manifestations vary but can include pain, paresthesia, or sensory loss.
Autonomic dysfunction appears to be relatively common, with many individuals having poor circulation (e.g., skin mottling, cold feet) and some having difficulties with temperature regulation.
Neuroimaging
Epilepsy is seen in ~40% of individuals
While age of onset is typically in childhood (median age of onset: 3.3 years), some individuals have their first seizure in adolescence.
Multiple seizure types are observed. Absence seizures are the most common, followed by grand mal seizures, atonic or drop seizures, and infantile spasms. Some individuals have specific seizure disorders such as electrical status epilepticus in sleep or Lennox-Gastaut syndrome. One person can have multiple different seizure types and frequency throughout the course of their life.
Seizure frequency can vary. Roughly one third of individuals with epilepsy have daily seizures, whereas some individuals have only one or two seizures in their lifetime.
EEG abnormalities can be observed even in individuals without clinical seizures.
Visual impairment
Refractive errors are common: 47% have either myopia or hyperopia with 14% having amblyopia.
Optic nerve hypoplasia is occasionally present. Optic nerve atrophy and degeneration will eventually occur in almost all individuals and is likely underreported. While large-scale surveys report optic nerve atrophy in close to 50% of affected individuals, one study comparing caregiver-reported diagnoses of optic atrophy and a comprehensive in-person evaluation found evidence of atrophy in 20 of 22 individuals despite it having been previously reported in only 10 of the 22 [
Sudnawa et al 2024].
Cerebral visual impairment and strabismus are both seen in close to one third of individuals.
Nystagmus is seen in 22% of individuals.
Cataracts are seen in ~10% of individuals.
Although rarely reported, deficits in color vision, visual fields, and depth perception appear to be common when specifically evaluated.
Growth
Musculoskeletal
Scoliosis was reported in 14% of individuals in one study, but as most study participants were relatively young (mean age: 9.9 years; median age: 7.3 years), this may be an underrepresentation as the cohort gets older [
Boyle et al 2021].
Contractures, seen in 10% of individuals, most commonly involve hips, ankles, fingers, and toes.
Although fractures are seen in 26% of individuals, this is likely related at least in part to the excessive clumsiness common in these individuals.
Gastrointestinal difficulties
Gastroesophageal reflux disease is seen in 34% of individuals.
Other findings include constipation (40%), diarrhea (17%), and irritable bowel syndrome (5%).
Genital abnormalities
Hearing impairment. While uncommon, some individuals have sensorineural hearing loss.
Additional features
Prognosis.
KIF1A-NDD is a progressive disorder. Individuals with KIF1A-NDD often live to adulthood; however, certain genotypes are consistently associated with shortened life span (see Genotype-Phenotype Correlations). Typical causes of death in KIF1A-NDD include seizures and respiratory failure in the setting of aspiration or an intercurrent infection.
Genotype-Phenotype Correlations
Kinesin-like protein KIF1A (KIF1A) is comprised of a motor domain (the first ~360 amino acids) and a tail domain (the remainder of the protein). Most disease-causing variants in both simple KIF1A-associated neurologic disorders (KAND) and KIF1A-NDD (also called complex KAND) occur in the motor domain, while pathogenic variants associated with hereditary sensory and autonomic neuropathy (HSAN KAND) and amyotrophic lateral sclerosis (ALS KAND) are more often in the tail domain [Boyle et al 2021, Ghafoor et al 2024, Zhao et al 2024] (see also Genetically Related Disorders).
Within the motor domain, certain highly conserved functional regions are involved in ATP and microtubule binding: the P loop (97-103), switch I (202-217), and switch II (248-325). Pathogenic variants in these regions of the motor domain are commonly seen in KIF1A-NDD and are often associated with increased disease severity [Boyle et al 2021].
Phenotypes associated with recurrent variants associated with severe phenotypes. One of the pathogenic variants associated with the most severe phenotype is c.757G>A (p.Glu253Lys); many affected individuals with this variant die in their first few years of life. The oldest known individual with this variant is not yet age 10 years at the time of writing [Nemani et al 2020, Boyle et al 2021].
Another variant consistently associated with a severe phenotype is c.296C>T (p.Thr99Met). This variant is also associated with reduced life span, though one individual with this variant is in their early 20s [Boyle et al 2021, Nicita et al 2021].
Individuals with either of the above two variants are largely non-verbal, non-ambulatory, and frequently have such profound hypotonia that they require gastrostomy tube placement.
Recurrent variants associated with milder phenotypes. Even though most pathogenic variants associated with KIF1A-NDD are de novo, the large number of recurrent variants has allowed for additional genotype-phenotype analysis. Morison et al [2026] examined the clinical findings associated with five common recurrent variants: c.32G>A (p.Arg11Gln), c.647G>A (p.Arg216His), c.760C>T (p.Arg254Trp), c.920G>A (p.Arg307Gln), and c.946C>T (p.Arg316Trp). Individuals with the p.Arg11Gln variant or the p.Arg216His variant had milder phenotypes, with many individuals able to combine spoken words at age 2-3 years. In contrast, individuals with the p.Arg254Trp variant reached the same milestone at age 4-5 years, while individuals with the p.Arg307Gln were largely unable to combine words. The p.Arg316Trp variant had a much more variable phenotype.
Nomenclature
KIF1A-NDD has also been referred to as progressive encephalopathy with edema, hypsarrhythmia, and optic atrophy (PEHO) and KIF1A-related Rett syndrome [Langlois et al 2016, Wang et al 2019].
Prevalence
About 300 individuals with KIF1A-NDD have been reported worldwide (see Clinical Description).
Management
No clinical practice guidelines for KIF1A-related neurodevelopmental disorder (KIF1A-NDD) have been published. In the absence of published guidelines, the following recommendations are based on the authors' personal experience managing individuals with this disorder.
Evaluations Following Initial Diagnosis
To establish the extent of disease and needs in an individual diagnosed with KIF1A-NDD, the evaluations summarized in Table 5 (if not performed as part of the evaluation that led to the diagnosis) are recommended.
Treatment of Manifestations
There is no cure for KIF1A-NDD. Supportive care to improve quality of life, maximize function, and reduce complications is recommended. This ideally involves multidisciplinary care by specialists in relevant fields (see Table 6).
Developmental Delay / Intellectual Disability Management Issues
The following information represents typical management recommendations for individuals with developmental delay / intellectual disability in the United States; standard recommendations may vary from country to country.
Ages 0-3 years. Referral to an early intervention program is recommended for access to occupational, physical, speech, and feeding therapy as well as infant mental health services, special educators, and sensory impairment specialists. In the US, early intervention is a federally funded program available in all states that provides in-home services to target individual therapy needs.
Ages 3-5 years. In the US, developmental preschool through the local public school district is recommended. Before placement, an evaluation is made to determine the services and therapies needed and an individualized education plan (IEP) is developed for those who qualify based on established motor, language, social, or cognitive delay. The early intervention program typically assists with this transition. Developmental preschool is center based; for children too medically unstable to attend, home-based services are provided.
All ages. Consultation with a developmental pediatrician is recommended to ensure the involvement of appropriate community, state, and educational agencies (US) and to support parents in maximizing quality of life. Some issues to consider:
IEP services:
An IEP provides specially designed instruction and related services to children who qualify.
IEP services will be reviewed annually to determine whether any changes are needed.
Special education law requires that children participating in an IEP be in the least restrictive environment feasible at school and included in general education as much as possible, when and where appropriate.
Vision and hearing consultants should be a part of the child's IEP team to support access to academic material.
PT, OT, and speech services will be provided in the IEP to the extent that the need affects the child's access to academic material. Beyond that, private supportive therapies based on the affected individual's needs may be considered. Specific recommendations regarding therapy can be made by a developmental pediatrician.
As a child enters their teens, a transition plan should be discussed and incorporated in the IEP. For those receiving IEP services, the public school district is required to provide services until age 21.
A 504 plan (Section 504: a US federal statute that prohibits discrimination based on disability) can be considered for those who require accommodations or modifications such as front-of-class seating, assistive technology devices, classroom scribes, extra time between classes, modified assignments, and enlarged text.
Developmental Disabilities Administration (DDA) enrollment is recommended. DDA is a US public agency that provides services and support to qualified individuals. Eligibility differs by state but is typically determined by diagnosis and/or associated cognitive/adaptive disabilities.
Families with limited income and resources may also qualify for supplemental security income (SSI) for their child with a disability.
Motor Dysfunction
Gross motor dysfunction
Physical therapy is recommended to maximize mobility and to reduce the risk for later-onset orthopedic complications (e.g., contractures, scoliosis, hip dislocation).
Consider use of durable medical equipment and positioning devices as needed (e.g., wheelchairs, walkers, bath chairs, orthotics, adaptive strollers).
Fine motor dysfunction. Occupational therapy is recommended for difficulty with fine motor skills that affect adaptive function such as feeding, grooming, dressing, and writing.
Speech, language, and communication issues. Speech-language evaluation should be considered early in development for children who have delayed communication milestones or who are not yet talking. Evaluation for alternative means of communication (e.g., augmentative and alternative communication [AAC]) is appropriate for individuals who have speech or receptive and expressive language difficulties. An AAC evaluation should be completed by a speech-language pathologist who has expertise in the area. This evaluation typically takes into account cognitive abilities, sensory impairments, and motor skills to determine the most appropriate form of communication. AAC devices can range from low-tech, such as picture exchange communication, to high-tech, such as voice-generating devices. Contrary to popular belief, AAC devices do not hinder verbal development of speech, but rather support optimal speech and language development. Many children will continue to require AAC into later childhood and adulthood, while some may use their AAC for a shorter time to help aid speech and language development.
Neurobehavioral/Psychiatric Concerns
Children may qualify for and benefit from interventions used in treatment of autism spectrum disorder, including applied behavior analysis (ABA). ABA therapy is targeted to the individual child's behavioral, social, and adaptive strengths and weaknesses and typically performed one on one with a board-certified behavior analyst.
Consultation with a developmental pediatrician may be helpful in guiding parents through appropriate behavior management strategies or providing prescription medications, such as medication used to treat attention-deficit/hyperactivity disorder, when necessary.
Concerns about serious aggressive or destructive behavior can be addressed by a pediatric psychiatrist.
While rare, additional psychiatric concerns including obsessive-compulsive disorder (OCD), anxiety, depression, and psychosis appear more commonly in adolescence and adulthood.
Surveillance
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in Table 7 are recommended.
Therapies Under Investigation
A small number of individuals with dominant-negative disease-causing variants in KIF1A are participating in an ongoing study of an allele-selective antisense oligonucleotide therapy to reduce expression of the pathogenic allele [Ziegler et al 2024]. Initial evaluations of the first recipient showed some improvement in seizures and gross motor skills, suggesting these therapies show some promise in altering the clinical outcome for affected individuals.
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.
Genetic Counseling
Autosomal Dominant Inheritance – Risk to Family Members
Parents of a proband
If the
proband appears to be the only affected family member (i.e., a
simplex case),
molecular genetic testing is recommended for the parents of the proband to evaluate their genetic status and inform
recurrence risk assessment. Note: A proband may appear to be the only affected family member because of failure to recognize the disorder in family members, reduced
penetrance, early death of a parent before the onset of symptoms, or late onset of the disease in an affected parent. Therefore,
de novo occurrence of a
KIF1A pathogenic variant cannot be confirmed unless molecular genetic testing has demonstrated that neither parent is
heterozygous for the
KIF1A pathogenic variant.
If the
pathogenic variant identified in the
proband is not identified in either parent and parental identity testing has confirmed biological maternity and paternity, the following possibilities should be considered:
Sibs of a proband. The risk to the sibs of the proband depends on the clinical/genetic status of the proband's parents:
If a parent of the
proband is affected and/or is known to have the
pathogenic variant identified in the proband, the risk to the sibs of inheriting the pathogenic variant is 50%.
Pathogenic variants in
KIF1A appear to have near complete
penetrance. While some
intrafamilial variability has been reported, affected sibs with the same pathogenic
KIF1A variant would be expected to show largely similar manifestations.
If the parents have not been tested for the
KIF1A pathogenic variant but are clinically unaffected, the risk to the sibs of a
proband appears to be low. However, sibs of a proband with clinically unaffected parents are still presumed to be at increased risk for
KIF1A-NDD because of the possibility of parental
gonadal mosaicism.
Offspring of a proband
Other family members. The risk to other family members depends on the status of the proband's parents: if a parent has the KIF1A pathogenic variant, the parent's family members may be at risk.
Autosomal Recessive Inheritance – Risk to Family Members
Parents of a proband
If a
pathogenic variant is detected in only one parent and parental identity testing has confirmed biological maternity and paternity, it is possible that one of the pathogenic variants identified in the
proband occurred as a
de novo event in the proband or as a
postzygotic de novo event in a mosaic parent [
Jónsson et al 2017]. If the proband appears to have
homozygous pathogenic variants (i.e., the same two pathogenic variants), additional possibilities to consider include:
Heterozygous parents of a child with
autosomal recessive KIF1A-NDD are asymptomatic and are not at risk of developing the disorder.
Sibs of a proband
If both parents are known to be
heterozygous for a
KIF1A pathogenic variant, each sib of an affected individual has at conception a 25% chance of being affected, a 50% chance of being an asymptomatic
carrier, and a 25% chance of being unaffected and not a carrier.
Heterozygous sibs of a child with
autosomal recessive KIF1A-NDD are asymptomatic and are not at risk of developing the disorder.
Offspring of a proband
Other family members. Each sib of the proband's parents is at a 50% risk of being a carrier of a KIF1A pathogenic variant.
Carrier detection. Carrier testing for at-risk relatives requires prior identification of the KIF1A pathogenic variants in the family.
Prenatal Testing and Preimplantation Genetic Testing
Once the KIF1A pathogenic variant(s) have been identified in an affected family member, prenatal and preimplantation genetic testing are possible.
Differences in perspective may exist among medical professionals and within families regarding the use of prenatal and preimplantation genetic testing. While most health care professionals would consider use of prenatal and preimplantation genetic testing to be a personal decision, discussion of these issues may be helpful.
Molecular Genetics
Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.
Table A.
KIF1A-Related Neurodevelopmental Disorder: Genes and Databases
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Data are compiled from the following standard references: gene from
HGNC;
chromosome locus from
OMIM;
protein from UniProt.
For a description of databases (Locus Specific, HGMD, ClinVar) to which links are provided, click
here.
Molecular Pathogenesis
KIF1A encodes kinesin-like protein KIF1A (KIF1A) is an ATP-dependent molecular motor protein that transports a variety of cargo along axonal microtubules [Chiba et al 2023]. KIF1A functions as a dimer when acting as a transporter; however, it is thought to be monomeric in solution. Most individuals with KIF1A-NDD have missense variants in the motor domain. Heterodimers of functional and disease-associated KIF1A proteins have reduced motility, suggesting many of these variants reduce transport by acting in a dominant-negative fashion. Depending on the specific residue involved, mutated proteins have been shown to have reduced binding to microtubules, reduced run length or velocity, or increased binding to microtubules resulting in a rigor state. Studies have shown a correlation between molecular mechanism of protein dysfunction and disease severity [Boyle et al 2021, Chiba et al 2023].
Mechanism of disease causation. Largely dominant-negative; however, mild phenotypes are associated with haploinsufficiency.
Table 8.
KIF1A Pathogenic Variants Referenced in This GeneReview
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Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.