Gene
SMCHD1
structural maintenance of chromosomes flexible hinge domain containing 1
- HGNC 29090(opens in a new tab)
- Ensembl gene ENSG00000101596(opens in a new tab)
- NCBI Gene 23347(opens in a new tab)
Summary
- Cytogenetic location
- 18p11.32
- Coordinates
- Chromosome 18: 2,655,726–2,805,017 (GRCh38)
- Exons
- 48 exons across 149.3 kb
- Protein
- 2,005 amino acids
- Also known as
- KIAA0650, FSHD2
- MANE Select transcript
- ENST00000320876.11NM_015295.3
- 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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Hypogonadotropic Hypogonadism
Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.
- ClinGen rates the link definitive
- 6 GenCC submitters rate it definitive or strong
How SMCHD1 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 8.8 kb of the gene's 149.3 kb; 6,018 of those bases code for the protein.
How a genome test reads SMCHD1
72
positions in SMCHD1 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 149.3 kb of SMCHD1, introns included, not only the 8.8 kb of exons.
Traits linked to SMCHD1
The Human Phenotype Ontology lists these as features of the rare conditions SMCHD1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Abnormal dental position
- Abnormality of the midface
- Absent nose
- Expressionless face
- Hyposmia
- Lost smell
- Missing nostrils
- Mono nostril
Show 21 more traits
- Unerupted adult teeth
- Blockage of the rear opening of the nasal cavity
- Decreased facial expression
- Decreased nasal size
- Decreased size of maxilla
- Eyelids stay open at night
- High palate
- Midface retrusion
- Paranasal sinus hypoplasia
- Pink eye
- Unopened tear duct
- Weakness of facial musculature
- Bad bite
- Bell's palsy
- Bifid uvula
- Cleft lip
- Cleft palate
- Dacryocystocele
- Decreased size of teeth
- Monobrow
- Submucous cleft hard palate
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.). SMCHD1 gene: structural maintenance of chromosomes flexible hinge domain containing 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/smchd1
Dante Labs. SMCHD1 gene: structural maintenance of chromosomes flexible hinge domain containing 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/smchd1
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