Gene
NSD2
nuclear receptor binding SET domain protein 2
- HGNC 12766(opens in a new tab)
- Ensembl gene ENSG00000109685(opens in a new tab)
- NCBI Gene 7468(opens in a new tab)
Summary
- Cytogenetic location
- 4p16.3
- Coordinates
- Chromosome 4: 1,871,393–1,982,192 (GRCh38)
- Exons
- 22 exons across 110.8 kb
- Protein
- 1,365 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- MMSET, KMT3G
- Previous symbols
- WHSC1
- MANE Select transcript
- ENST00000508803.6NM_001042424.3
- 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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Intellectual Disability
- Wolf-Hirschhorn syndromeAutosomal dominant
A condition caused by deletion of the end of chromosome 4p that causes growth restriction, intellectual disability, seizures and distinctive facial features.
- 1 GenCC submitter rates it definitive or strong
One of 233 genes linked to it
- ClinGen rates the link definitive
- 1 GenCC submitter rates 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 NSD2 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 7.6 kb of the gene's 110.8 kb; 4,098 of those bases code for the protein.
How a genome test reads NSD2
51
positions in NSD2 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 110.8 kb of NSD2, introns included, not only the 7.6 kb of exons.
Traits linked to NSD2
The Human Phenotype Ontology lists these as features of the rare conditions NSD2 can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Abnormally small head
- Almond shaped eyes
- Corners of eye widely separated
- Decreased volume of lip
- Depressed nasal bridge
- Eye folds
- Fullness around the eyes
- High forehead
Show 31 more traits
- Little lower jaw
- Long philtrum
- Short chin
- Short philtrum
- Upward slanting of the opening between the eyelids
- Abnormal lip
- Abnormality of the mouth
- Abnormality of the philtrum
- Downturned corners of mouth
- Downward slanting of the opening between the eyelids
- Failure of development of between one and six teeth
- Frontal bossing
- High frontal hairline
- Highly arched eyebrow
- Long, narrow head
- Low hairline at back of neck
- Wide nasal bridge
- Abnormality of craniofacial shape
- Beaked nose
- Cleft of the mouth
- Cleft upper lip
- Cranial defect
- Delayed eruption of teeth
- Pit in front of the ear
- Prominent area between the eyebrows
- Prominent forehead
- Short upper lip
- Skin tag in front of the ear
- Taurodontia
- Cleft palate
- Webbed neck
Abnormality of the nervous system
- Aggressive behavior
- Anxiety
- Autism spectrum disorder
- Global developmental delay
- Intellectual disability
- More active than typical
- Repetitive movements
- Ataxia
Show 14 more traits
- EEG abnormality
- Epilepsy
- Intellectual disability, severe
- Difficulty sleeping
- Morphological central nervous system abnormality
- Tethered cord
- Abnormality of movement
- Absent/small cerebellum
- Agenesis of corpus callosum
- Too much cerebrospinal fluid in the brain
- Absent septum pellucidum
- Cavum septum pellucidum
- Periventricular cysts
- Ventriculomegaly
Abnormality of the genitourinary system
- Hypospadias
- Abnormality of the kidney
- Bilateral renal hypoplasia
- Hyperechogenic kidneys
- Undescended testes
- Abnormality of the genitourinary system
- Abnormality of the reproductive system
- Absent uterus
Show 2 more traits
Abnormality of the digestive system
- Enlarged liver
- Feeding difficulties
- Chronic constipation
- Inability to properly digest food due to lack of pancreatic digestive enzymes
- Abdominal situs inversus
- Abnormality of the gallbladder
- Biliary tract abnormality
- Acid reflux
Show 1 more trait
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.). NSD2 gene: nuclear receptor binding SET domain protein 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/nsd2
Dante Labs. NSD2 gene: nuclear receptor binding SET domain protein 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nsd2
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