Gene
COL12A1
collagen type XII alpha 1 chain
- HGNC 2188(opens in a new tab)
- Ensembl gene ENSG00000111799(opens in a new tab)
- NCBI Gene 1303(opens in a new tab)
Summary
- Cytogenetic location
- 6q13-q14.1
- Coordinates
- Chromosome 6: 75,084,326–75,206,053 (GRCh38)
- Exons
- 66 exons across 121.7 kb
- Protein
- 3,063 amino acids
- Previous symbols
- COL12A1L
- MANE Select transcript
- ENST00000322507.13NM_004370.6
- Locus type
- gene with protein product
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
Congenital Muscular Dystrophies
- Congenital muscular dystrophy
A group of muscular dystrophies with onset at birth or in infancy, including dystroglycanopathies (such as FKRP, FKTN and POMT1/2-related forms).
- 4 GenCC submitters rate it definitive or strong
Ehlers-Danlos Syndrome
- 3 GenCC submitters rate it definitive or strong
How COL12A1 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 11.7 kb of the gene's 121.7 kb; 9,192 of those bases code for the protein.
How a genome test reads COL12A1
109
positions in COL12A1 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 121.7 kb of COL12A1, introns included, not only the 11.7 kb of exons.
Traits linked to COL12A1
The Human Phenotype Ontology lists these as features of the rare conditions COL12A1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the musculoskeletal system
- Distal joint hypermobility
- Double-Jointed
- Flexed joint that cannot be straightened
- Hunched back
- Increased variability in muscle fiber diameter
- Low muscle tone
- Muscle weakness
- Proximal neurogenic muscle weakness
Show 32 more traits
- Abnormal muscle fiber morphology
- EMG: myopathic abnormalities
- Generalized muscle weakness
- Increased endomysial connective tissue
- Increased wrist mobility
- Muscular dystrophy
- Progressive proximal muscle weakness
- Reduced muscle collagen VI
- Reduced spine movement
- Diffuse skeletal muscle wasting
- Frequent falls
- Generalized decreased muscle tone
- Kyphoscoliosis
- Low muscle tone, in neonatal onset
- Multiple joint contractures
- Muscle degeneration
- Muscle tissue disease
- Neck muscle weakness
- Scoliosis
- Weak diaphragm
- Weakness of outermost muscles
- Axial muscle weakness
- Congenital contracture
- Decreased muscle mass
- Excessive inward curvature of lower spine
- Funnel chest
- Gowers sign
- Prominent swayback
- Reduced maximal expiratory pressure
- Rimmed vacuoles
- Shoulder flexion contracture
- Difficulty running
Abnormality of limbs
- Increased laxity of fingers
- Ankle flexion contracture
- Elbow flexion contracture
- Hip dislocation
- Inability to straighten knee
- Interphalangeal joint contracture of finger
- Inward turned thumb
- Limb-girdle muscle weakness
Show 18 more traits
- Long toe
- Permanent flexion of the finger
- Pes valgus
- Quadriceps weakness
- Slender finger
- Wrist flexion contracture
- Club feet
- Congenital bilateral hip dislocation
- Congenital finger flexion contractures
- Contractures of the foot joints
- Curved toe bone
- Dropped arches
- Foot drop
- Joint contracture of the hand
- Partial knee cap dislocation
- Shortening of the achilles tendon
- Tapered finger
- Winged shoulder blade
Abnormality of head or neck
- Abnormality of the palate
- Bell's palsy
- High palate
- Little lower jaw
- Short neck
- Wry neck
- Congenital muscular torticollis
- High, narrow palate
Show 1 more trait
Abnormality of the nervous system
- Motor delay
- Stooped posture
- Abnormal gait
- Absent reflexes
- Delayed ability to stand
- Delayed ability to walk
- Delayed fine motor development
- Toe walking
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.). COL12A1 gene: collagen type XII alpha 1 chain. Retrieved 16 October 2026, from https://dantelabs.com/genes/col12a1
Dante Labs. COL12A1 gene: collagen type XII alpha 1 chain [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/col12a1
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