Gene
ATP1A2
ATPase Na+/K+ transporting subunit alpha 2
- HGNC 800(opens in a new tab)
- Ensembl gene ENSG00000018625(opens in a new tab)
- NCBI Gene 477(opens in a new tab)
Summary
- Cytogenetic location
- 1q23.2
- Coordinates
- Chromosome 1: 160,115,759–160,143,591 (GRCh38)
- Exons
- 23 exons across 27.8 kb
- Protein
- 1,020 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- FHM2
- Previous symbols
- MHP2
- MANE Select transcript
- ENST00000361216.8NM_000702.4
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Get my Genome TestCurated reports relevant to this gene
Familial Hemiplegic Migraine
- Hemiplegic Migraine-Developmental And Epileptic Encephalopathy Spectrum
A spectrum in which individuals may present with phenotypes ranging from hemiplegic migraines without epilepsy to developmental and epileptic encephalopathy with or without episodic hemiplegia or other forms of paresis. Symptoms and severity may vary within families.
- ClinGen rates the link definitive
- 1 GenCC submitter rates it definitive or strong
- Migraine, Familial Hemiplegic, 2Autosomal dominant
Any familial or sporadic hemiplegic migraine in which the cause of the disease is a mutation in the ATP1A2 gene.
- 5 GenCC submitters rate it definitive or strong
- Autosomal dominant
A migraine disorder characterized by individual and family history of aura that includes motor weakness.
- ClinGen rates the link definitive
- 6 GenCC submitters rate it definitive or strong
- Familial Or Sporadic Hemiplegic MigraineAutosomal dominant
Hemiplegic migraine (HM) is a rare variety of migraine with aura characterized by the presence of a motor weakness during the aura. Hemiplegic migraine has two main forms depending on the familial history: patients with at least one first- or second-degree relative who has aura including motor weakness have familial hemiplegic migraine (FHM); patients without such familial history have sporadic hemiplegic migraine (SHM).
- ClinGen rates the link definitive
- 6 GenCC submitters rate it definitive or strong
Broader groupings
Epilepsy (Full Panel)
- Epilepsy
One of 171 genes linked to it
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
- ClinGen rates the link definitive
- 4 GenCC submitters rate it definitive or strong
Inheritance
- Autosomal dominant
- One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.
How ATP1A2 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 5.4 kb of the gene's 27.8 kb; 3,063 of those bases code for the protein.
How a genome test reads ATP1A2
121
positions in ATP1A2 where ClinVar classes a change as pathogenic or likely pathogenic
6 of them (5%) fall in regions short reads find hard.
- Low mappability (6 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
A whole genome covers all 27.8 kb of ATP1A2, introns included, not only the 5.4 kb of exons.
Traits linked to ATP1A2
The Human Phenotype Ontology lists these as features of the rare conditions ATP1A2 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Abnormal cortical gyration
- Aplasia/Hypoplasia of the pyramidal tract
- Difficulty finding words
- Episodic hemiplegia
- Episodic quadriplegia
- Migraine
- More grooves in brain
- Weakness of one side of body
Show 87 more traits
- Abnormal speech pattern
- Confusion
- EEG abnormality
- Encephalopathy
- Focal motor seizure
- Focal sensory seizure
- Global developmental delay
- Grand mal seizures
- Intellectual disability
- Migraine with aura
- Abnormal autonomic nervous system physiology
- Abnormality of coordination
- Ataxia
- Balance impairment
- Behavioral abnormality
- Coma
- Complex febrile seizure
- CSF lymphocytic pleiocytosis
- CSF pleocytosis
- Decreased reflex response
- Delayed speech and language development
- Difficulty articulating speech
- Dissociated sensory loss
- Dystonia
- EEG with multifocal slow activity
- Epilepsy
- Focal manual automatism seizure
- Focal pedal automatism seizure
- Involuntary movements
- Loss of developmental milestones
- Neurodevelopmental delay
- Pins and needles feeling
- Progressive gait ataxia
- Refractory status epilepticus
- Seizure affecting one half of brain
- Tetraparesis
- Abnormal corpus callosum morphology
- Abnormal gait
- Abnormal myelination
- Abnormal pyramidal sign
- Absent reflexes
- Absent speech development
- Aggressive behavior
- Alien limb phenomenon
- Attention deficit
- Autism
- Bilateral tonic-clonic seizure with focal onset
- Brain degeneration
- Bulbar signs
- Can't control feelings
- Chorea
- Choreoathetosis
- Clonic seizure
- Decreased vigilance
- Degeneration of cerebellum
- Degeneration of cerebrum
- Diminished deep tendon reflex
- Disorder of involuntary muscle movements
- EEG with burst suppression
- EEG with generalized sharp slow waves
- Headache
- Hypsarrhythmia
- Impaired temperature sensation
- Impulsivity
- Inability to coordinate movements when walking
- Increased reflexes
- Jerking
- Lack of coordination of movement
- Language impairment
- Mental deterioration
- Paralysis on one side of body
- Paroxysmal dyskinesia
- Pauses in breathing while sleeping
- Perisylvian polymicrogyria
- Poor eye contact
- Repeated seizures without recovery between them
- Spontaneous pain sensation
- Thick corpus callosum
- Thin corpus callosum
- Tremor
- Unsteady walk
- Worsening neurological symptoms
- EEG with focal sharp waves
- Apraxia
- Brain imaging abnormality
- Drowsiness
- Episodic ataxia
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). ATP1A2 gene: ATPase Na+/K+ transporting subunit alpha 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp1a2
Dante Labs. ATP1A2 gene: ATPase Na+/K+ transporting subunit alpha 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp1a2
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