Gene
NSD1
nuclear receptor binding SET domain protein 1
- HGNC 14234(opens in a new tab)
- Ensembl gene ENSG00000165671(opens in a new tab)
- NCBI Gene 64324(opens in a new tab)
Summary
- Cytogenetic location
- 5q35.3
- Coordinates
- Chromosome 5: 177,133,773–177,300,213 (GRCh38)
- Exons
- 23 exons across 166.4 kb
- Protein
- 2,696 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- ARA267, FLJ22263, KMT3B
- Previous symbols
- STO
- MANE Select transcript
- ENST00000439151.7NM_022455.5
- 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
Imprinting Disorders: Prader-Willi, Silver-Russell and Beckwith-Wiedemann
- Beckwith-Wiedemann syndrome
An overgrowth disorder caused by imprinting changes at 11p15 (and sometimes CDKN1C variants) that can cause large birth size, an enlarged tongue, abdominal wall defects and a higher risk of childhood tumours such as Wilms tumour.
- 1 GenCC submitter rates it definitive or strong
What knowing changes
Diagnosis leads to childhood tumour surveillance, including abdominal ultrasound.
Overgrowth Syndromes (Sotos, Weaver, Tatton-Brown-Rahman, Malan)
- Sotos syndromeAutosomal dominant
An overgrowth syndrome caused by NSD1 variants or deletions, with a large head, tall stature in childhood, characteristic facial features and learning difficulties.
- ClinGen rates the link definitive
- 6 GenCC submitters rate it definitive or strong
What knowing changes
Knowing allows monitoring for associated problems, including a modestly increased risk of some childhood tumours.
Broader groupings
Hypertrophic Cardiomyopathy
- Autosomal dominant
One of 62 genes linked to it
A condition in which the myocardium is hypertrophied without an obvious cause. The hypertrophy is generally asymmetric and may be associated with obstruction of the ventricular outflow tract.
- 1 GenCC submitter rates it definitive or strong
What knowing changes
Beta-blockers, non-dihydropyridine calcium channel blockers, activity restriction, genetic counseling
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 NSD1 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 13 kb of the gene's 166.4 kb; 8,091 of those bases code for the protein.
How a genome test reads NSD1
364
positions in NSD1 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 166.4 kb of NSD1, introns included, not only the 13 kb of exons.
Traits linked to NSD1
The Human Phenotype Ontology lists these as features of the rare conditions NSD1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Absence of scalp hair
- Bad bite
- Big head present at birth
- Big lower jaw
- Broad forehead
- Broad nasal tip
- Broad nostril
- Dental crowding
Show 46 more traits
- Downward slanting of the opening between the eyelids
- Excessive wear and tear on teeth
- Eye folds
- Frontal bossing
- High forehead
- High frontal hairline
- High palate
- Long, narrow head
- Narrow eyelid opening
- Narrow face
- Narrow forehead
- Narrow jaw
- Nasal tip, upturned
- Sparse eyebrow
- Abnormally small head
- Big calvaria
- Coarse facial features
- Failure of development of between one and six teeth
- Little lower jaw
- Long philtrum
- Pointed chin
- Prominent forehead
- Receding chin
- Deep bite
- Deep philtrum
- Depressed nasal bridge
- Increased head circumference
- Increased nuchal translucency
- Long face
- Round face
- Short neck
- Sparse scalp hair at front of head
- Tall chin
- Triangular face
- Wide fontanelles
- Abnormal dentition
- Cross bite
- Ectopic tooth eruption
- Enlarged cisterna magna
- Thin dental enamel
- Absence of adult teeth
- Deformity of the skull
- Delayed eruption of permanent teeth
- Early eruption of teeth
- High, narrow palate
- Narrow palate
Abnormality of the nervous system
- Absent speech development
- Aggressive behavior
- Attention deficit
- Brisk reflexes
- Clonus
- Cognitive impairment
- Delayed ability to walk
- Fluid-filled sac located in membrane surrounding brain or spinal cord
Show 35 more traits
- Lateral ventricle dilatation
- Myelomeningocele
- Stuttering
- Thin corpus callosum
- Ventriculomegaly
- Abnormally low-pitched voice
- Global developmental delay
- Intellectual disability
- Specific learning disability
- Behavioral abnormality
- Brain imaging abnormality
- Delayed speech and language development
- Epilepsy
- Intellectual disability, mild
- IQ between 34 and 49
- Motor delay
- Anxiety
- Aplasia/Hypoplasia of the corpus callosum
- Autism spectrum disorder
- Brief seizures with staring spells
- Cavum septum pellucidum
- Cerebellar vermis hypoplasia
- Degeneration of cerebrum
- Difficulty making arithmetical calculations
- Focal impaired awareness seizure
- Generalized myoclonic seizure
- Grand mal seizures
- Incoordination
- Intellectual disability, severe
- Tremor
- Astrocytoma
- Cancer of early nerve cells
- Communication delay
- Increased reflexes
- Partial agenesis of the corpus callosum
Abnormality of limbs
- Fractured carpal bone
- Large hands
- Long foot
- Single transverse palmar crease
- Abnormality of the wide portion of a long bone
- Increased arm span
- Pes valgus
- Broad foot
Show 15 more traits
Abnormality of the integument
- Blue discoloration of the skin
- Abnormal fingernails
- Deep-set nails
- Loose redundant skin
- Thin nail
- Underdeveloped toenails
- Fine hair
- Flushing
Show 3 more traits
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.). NSD1 gene: nuclear receptor binding SET domain protein 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/nsd1
Dante Labs. NSD1 gene: nuclear receptor binding SET domain protein 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nsd1
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