Gene
SMC1A
structural maintenance of chromosomes 1A
- HGNC 11111(opens in a new tab)
- Ensembl gene ENSG00000072501(opens in a new tab)
- NCBI Gene 8243(opens in a new tab)
Summary
- Cytogenetic location
- Xp11.22
- Coordinates
- Chromosome X: 53,374,149–53,422,654 (GRCh38)
- Exons
- 25 exons across 48.5 kb
- Protein
- 1,233 amino acids
- Also known as
- DXS423E, KIAA0178, SB1.8, Smcb
- Previous symbols
- SMC1L1
- MANE Select transcript
- ENST00000322213.9NM_006306.4
- 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
Cornelia de Lange Syndrome
A developmental disorder caused by variants in NIPBL, SMC1A, SMC3, RAD21, HDAC8 or BRD4, with a wide range of severity.
- 3 GenCC submitters rate it definitive or strong
What knowing changes
Diagnosis guides monitoring for associated problems such as reflux, heart defects, hearing and vision issues.
Epilepsy (Full Panel)
- X-Linked Complex Neurodevelopmental Disorder
A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.
- ClinGen rates the link definitive
- 1 GenCC submitter rates it definitive or strong
- 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.
- 3 GenCC submitters rate it definitive or strong
How SMC1A 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 9.7 kb of the gene's 48.5 kb; 3,702 of those bases code for the protein.
How a genome test reads SMC1A
155
positions in SMC1A where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 48.5 kb of SMC1A, introns included, not only the 9.7 kb of exons.
Traits linked to SMC1A
The Human Phenotype Ontology lists these as features of the rare conditions SMC1A can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Absent speech development
- Delayed ability to walk
- Delayed speech and language development
- EEG abnormality
- Epilepsy
- Global developmental delay
- Grand mal seizures
- Hypsarrhythmia
Show 70 more traits
- Infantile spasms
- Multifocal seizures
- Poor eye contact
- Repetitive movements
- Seizure affecting one half of brain
- Severe global developmental delay
- Abnormal gait
- Abnormality of movement
- Abnormally low-pitched voice
- Agitation
- Autism spectrum disorder
- Difficulty sleeping
- Intellectual disability
- Intellectual disability, severe
- Involuntary movements
- Loss of developmental milestones
- Loss of speech
- Stereotypical hand wringing
- Abnormal central motor function
- Abnormal morphology of the olfactory bulb
- Abnormal shape of brainstem
- Abnormal speech pattern
- Abnormality of the autonomic nervous system
- Anxiety
- Aplasia of the falx cerebri
- Apraxia
- Attention deficit
- Behavioral abnormality
- Depression
- Dystonia
- Hand apraxia
- Inability to coordinate movements when walking
- Inability to speak
- Inability to walk
- Irritability
- Lack of feeling, emotion, interest
- Lethargy
- Limb dystonia
- Limb myoclonus
- Loss of ability to walk
- Neonatal seizure
- Neural tube defect
- Obsessive compulsive behavior
- Oromotor apraxia
- Poor social interactions
- Restrictive behavior
- Sleep-wake cycle disturbance
- Specific learning disability
- Tongue thrusting
- Absent/small cerebellum
- Agenesis of corpus callosum
- Autism
- Decrease in size of the outer layer of the brain due to loss of brain cells
- Delayed motor skills
- Developmental stagnation
- Generalized myoclonic seizure
- Impaired pain sensation
- Inappropriate crying
- Inappropriate laughter
- Intellectual disability, mild
- Panic attack
- Peripheral neuropathy
- Pill-rolling tremor
- Poor speech
- Semilobar holoprosencephaly
- Too much cerebrospinal fluid in the brain
- Tremor
- Underdevelopment of part of brain called corpus callosum
- Ventriculomegaly
- Cognitive impairment
Abnormality of head or neck
- Abnormally small head
- Dental crowding
- Highly arched eyebrow
- Midface retrusion
- Monobrow
- Narrow nose
- Receding chin
- Round face
Show 38 more traits
- Short nose
- Triangular face
- Broad head shape
- Curly eyelashes
- Decreased volume of lip
- Delayed eruption of teeth
- Depressed nasal bridge
- Downturned corners of mouth
- High palate
- Little lower jaw
- Long eyelashes
- Long philtrum
- Low frontal hairline
- Low hairline at back of neck
- Nasal tip, upturned
- Short neck
- Thick eyebrow
- Widely spaced teeth
- Bifid uvula
- Central cleft upper lip
- Cleft palate
- Development of small head that was not present at birth
- Flat nose
- Inflammation of eyelids
- Smooth philtrum
- Big calvaria
- Blockage of the rear opening of the nasal cavity
- Downward slanting of the opening between the eyelids
- Facial asymmetry
- Increased nuchal translucency
- Mono nostril
- Narrow forehead
- Only one upper front tooth
- Proboscis
- Short philtrum
- Thin red part of the upper lip
- Upward slanting of the opening between the eyelids
- Prominent nasal bridge
Abnormality of limbs
- Curvature of digit
- Short foot
- Small hand
- Attachment of thumb close to wrist
- Fused toes
- Shortened 1st long bone of hand
- Smaller or shorter than typical limbs
- Bilateral single transverse palmar creases
Show 14 more traits
- Curvature of little finger
- Elbow dislocation
- Fused forearm bones
- Abnormal morphology of ulna
- Abnormality of limbs
- Broad big toe
- Contracture of the proximal interphalangeal joint of the 3rd finger
- Hip dislocation
- Oligodactyly
- Talipes
- Tapered finger
- Webbed first and second toes
- Limited elbow movement
- Short fingers or toes
Abnormality of the musculoskeletal system
- Congenital diaphragmatic hernia
- Generalized decreased muscle tone
- Low muscle tone in trunk
- Permanent flexion of the finger or toe
- Scoliosis
- Spastic tetraparesis
- Spasticity and rigidity of muscles
- Delayed bone maturation
Show 12 more traits
- Functional motor deficit
- Abnormal muscle tone
- Decreased muscle tone in infant
- Involuntary muscle stiffness, contraction, or spasm
- Joint stiffness
- Low muscle tone
- Abnormal formation of the hip
- Abnormality of the skeletal system
- Flexed joint that cannot be straightened
- Funnel chest
- Hunched back
- Low muscle tone, in neonatal onset
Abnormality of the genitourinary system
- Hypospadias
- Multicystic kidney dysplasia
- Small labia majora
- Underdeveloped penis
- Undescended testes
- Vesicoureteral reflux
- Abnormality of the genitourinary system
- Abnormality of the uterus
Show 2 more traits
Abnormality of the cardiovascular system
- An opening in the wall separating the top two chambers of the heart
- Cutis marmorata
- Abnormal cardiovascular system morphology
- Abnormal heart rate variability
- Abnormality of the heart
- Enlarged and thickened heart muscle
- Hole in heart wall separating two lower heart chambers
- Partial anomalous pulmonary venous return
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.). SMC1A gene: structural maintenance of chromosomes 1A. Retrieved 17 October 2026, from https://dantelabs.com/genes/smc1a
Dante Labs. SMC1A gene: structural maintenance of chromosomes 1A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/smc1a
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