Gene
SIN3A
SIN3 transcription regulator family member A
- HGNC 19353(opens in a new tab)
- Ensembl gene ENSG00000169375(opens in a new tab)
- NCBI Gene 25942(opens in a new tab)
Summary
- Cytogenetic location
- 15q24.2
- Coordinates
- Chromosome 15: 75,369,379–75,451,690 (GRCh38)
- Exons
- 21 exons across 82.3 kb
- Protein
- 1,273 amino acids
- Also known as
- KIAA0700, DKFZP434K2235
- MANE Select transcript
- ENST00000394947.8NM_001145358.2
- 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
One of 233 genes linked to it
- ClinGen rates the link definitive
- 3 GenCC submitters rate it definitive or strong
How SIN3A 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 6.7 kb of the gene's 82.3 kb; 3,822 of those bases code for the protein.
How a genome test reads SIN3A
55
positions in SIN3A where ClinVar classes a change as pathogenic or likely pathogenic
2 of them (3.6%) fall in regions short reads find hard.
- Low mappability (2 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
- Segmental duplications (2 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.
A whole genome covers all 82.3 kb of SIN3A, introns included, not only the 6.7 kb of exons.
Traits linked to SIN3A
The Human Phenotype Ontology lists these as features of the rare conditions SIN3A can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Long face
- Long philtrum
- Wide nasal bridge
- Abnormal facial shape
- Downward slanting of the opening between the eyelids
- Abnormally small head
- Broad eyebrow
- Broad forehead
Show 35 more traits
- Decreased head circumference
- Eye folds
- High frontal hairline
- Pointed chin
- Smooth philtrum
- Abnormal dentition
- Abnormality of the palate
- Big maxilla
- Branchial fistula
- Decreased depth of eye sockets
- Depressed nasal bridge
- Facial asymmetry
- Frontal bossing
- Full lower lip
- High forehead
- High palate
- Narrow mouth
- Nasal tip, upturned
- Overhanging nasal tip
- Prominent forehead
- Prominent nasal bridge
- Short nose
- Short opening between the eyelids
- Short philtrum
- Thin red part of the upper lip
- Triangular face
- Wide nasal base
- Flared nostrils
- High, narrow palate
- Medial flaring of the eyebrow
- Narrow face
- Open mouth
- Small retruded chin
- Underdeveloped tissue around nostril
- Wide nose
Abnormality of the nervous system
- Aggressive behavior
- Incoordination
- Intellectual disability, severe
- More active than typical
- Brain imaging abnormality
- Global developmental delay
- Intellectual disability, mild
- Autism
Show 25 more traits
- Autism spectrum disorder
- Behavioral abnormality
- Delayed speech and language development
- Intellectual disability
- Mild malformation of cortical development
- Motor delay
- Ventriculomegaly
- Abnormal cerebral white matter morphology
- Anxiety
- Bilateral polymicrogyria
- Cortical dysplasia
- Delayed CNS myelination
- Delayed fine motor development
- Dysplastic corpus callosum
- Epilepsy
- Non-epileptic seizure
- Obsessive compulsive behavior
- Pauses in breathing while sleeping
- Short attention span
- Myelomeningocele
- Attention deficit
- Conspicuously happy disposition
- Difficulty sleeping
- Loss of developmental milestones
- Underdevelopment of part of brain called corpus callosum
Abnormality of the eye
- Cross-eyed
- Wide-set eyes
- Clouding of the lens of the eye
- Deeply set eye
- Farsightedness
- Involuntary, rapid, rhythmic eye movements
- Notched pupil
- Cat eye
Show 2 more traits
Abnormality of the ear
- Abnormality of the outer ear
- Hearing impairment
- Glue ear
- Large ears
- Prominent ear
- Sensorineural hearing impairment
- Thickened helices
- Uplifted earlobe
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.). SIN3A gene: SIN3 transcription regulator family member A. Retrieved 16 October 2026, from https://dantelabs.com/genes/sin3a
Dante Labs. SIN3A gene: SIN3 transcription regulator family member A [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/sin3a
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