COL2A1
collagen type II alpha 1 chain, the group of Collagens
Basic information
Region (hg38): 12:47972966-48004554
Previous symbols: [ "SEDC", "AOM" ]
Links
Phenotypes
GenCC
Source:
- Stickler syndrome type 1 (Definitive), mode of inheritance: AD
- Stickler syndrome type 1 (Strong), mode of inheritance: AD
- Kniest dysplasia (Definitive), mode of inheritance: AD
- achondrogenesis type II (Definitive), mode of inheritance: AD
- platyspondylic dysplasia, Torrance type (Definitive), mode of inheritance: AD
- Stickler syndrome, type I, nonsyndromic ocular (Definitive), mode of inheritance: AD
- spondyloperipheral dysplasia (Definitive), mode of inheritance: AD
- spondyloepimetaphyseal dysplasia, Strudwick type (Definitive), mode of inheritance: AD
- spondyloepiphyseal dysplasia congenita (Definitive), mode of inheritance: AD
- Stickler syndrome type 1 (Strong), mode of inheritance: AD
- spondyloepiphyseal dysplasia with metatarsal shortening (Definitive), mode of inheritance: AD
- achondrogenesis type II (Strong), mode of inheritance: AD
- Legg-Calve-Perthes disease (Supportive), mode of inheritance: AD
- Kniest dysplasia (Supportive), mode of inheritance: AD
- spondyloperipheral dysplasia (Supportive), mode of inheritance: AD
- platyspondylic dysplasia, Torrance type (Supportive), mode of inheritance: AD
- dysspondyloenchondromatosis (Supportive), mode of inheritance: AD
- familial avascular necrosis of femoral head (Supportive), mode of inheritance: AD
- Stickler syndrome type 1 (Supportive), mode of inheritance: AD
- mild spondyloepiphyseal dysplasia due to COL2A1 mutation with early-onset osteoarthritis (Supportive), mode of inheritance: AD
- achondrogenesis type II (Supportive), mode of inheritance: AD
- hypochondrogenesis (Supportive), mode of inheritance: AD
- spondylometaphyseal dysplasia, Schmidt type (Supportive), mode of inheritance: AD
- spondyloepimetaphyseal dysplasia, Strudwick type (Supportive), mode of inheritance: AD
- spondyloepiphyseal dysplasia congenita (Supportive), mode of inheritance: AD
- spondyloepiphyseal dysplasia with metatarsal shortening (Supportive), mode of inheritance: AD
- multiple epiphyseal dysplasia, Beighton type (Supportive), mode of inheritance: AD
- autosomal dominant rhegmatogenous retinal detachment (Supportive), mode of inheritance: AD
- spondyloepiphyseal dysplasia, Stanescu type (Supportive), mode of inheritance: AD
- otospondylomegaepiphyseal dysplasia (Limited), mode of inheritance: AR
- spondyloepiphyseal dysplasia with metatarsal shortening (Strong), mode of inheritance: AD
- Kniest dysplasia (Strong), mode of inheritance: AD
- Legg-Calve-Perthes disease (Strong), mode of inheritance: AD
- mild spondyloepiphyseal dysplasia due to COL2A1 mutation with early-onset osteoarthritis (Strong), mode of inheritance: AD
- spondyloepiphyseal dysplasia congenita (Definitive), mode of inheritance: AR
- multiple epiphyseal dysplasia, Beighton type (Limited), mode of inheritance: AD
- achondrogenesis type II (Strong), mode of inheritance: AD
- otospondylomegaepiphyseal dysplasia, autosomal recessive (Limited), mode of inheritance: AD
- spondyloepiphyseal dysplasia congenita (Strong), mode of inheritance: AD
- otospondylomegaepiphyseal dysplasia, autosomal recessive (Strong), mode of inheritance: AR
- Stickler syndrome, type I, nonsyndromic ocular (Strong), mode of inheritance: AD
- avascular necrosis of femoral head, primary, 1 (Strong), mode of inheritance: AD
- vitreoretinopathy with phalangeal epiphyseal dysplasia (Limited), mode of inheritance: Unknown
- spondyloepiphyseal dysplasia, Stanescu type (Moderate), mode of inheritance: AD
- spondyloepiphyseal dysplasia congenita (Definitive), mode of inheritance: AD
- achondrogenesis type II (Definitive), mode of inheritance: AD
- Kniest dysplasia (Definitive), mode of inheritance: AD
- spondyloepiphyseal dysplasia with metatarsal shortening (Moderate), mode of inheritance: AD
- Stickler syndrome type 1 (Definitive), mode of inheritance: AD
- platyspondylic dysplasia, Torrance type (Definitive), mode of inheritance: AD
- spondyloperipheral dysplasia (Definitive), mode of inheritance: AD
- spondylometaphyseal dysplasia (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Stickler syndrome, type I; Czech dysplasia; Otospondylomegaepiphyseal dysplasia; Epiphyseal dysplasia, multiple, with myopia and deafness | AD | Audiologic/Otolaryngologic; Ophthalmologic | Though the condition may be recognizable, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Avoidance of risk factors related to ocular manifestations (eg, contact sports) is indicated; In Avascular necrosis of femoral head, primary, identifying carriers before the onset of clinical symptoms can allow interventions in order to delay disease progression | Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Ophthalmologic | 14299791; 5582025; 4568361; 4214536; 699354; 514691; 7036745; 6628450; 6496567; 4014370; 3728560; 2572591; 1975693; 2300123; 1677770; 1671807; 1429602; 1444917; 8434604; 8325895; 8317498; 8737653; 7981752; 7700721; 7874117; 7757081; 7550321; 7847372; 8737653; 8723097; 9800905; 10486316; 10406661; 10745044; 10982970; 11812423; 12939326; 12544472; 12884428; 15266623; 15895462; 15316962; 14729840; 15930420; 16189708; 15671297; 15316962; 16088915; 15643621; 17726487; 16752401; 16155195; 17394019; 17437277; 17509551; 17721977; 18553548; 19764028 ; 20131279; 20583175; 20513134; 21671384; 21204228; 20301479; 21924244; 21332586; 20179744; 26183434; 26420734 |
| The condition can include varying degrees/types of early hearing loss in some conditions, such as Stickler syndrome and Otospondylomegaepiphyseal dysplasia , while in others, such as Czech dysplasia, the hearing loss typically occurs much later |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2199 variants)
- Stickler syndrome type 1 (227 variants)
- not specified (129 variants)
- Type II Collagenopathies (124 variants)
- Connective tissue disorder (72 variants)
- Inborn genetic diseases (44 variants)
- Spondyloepiphyseal dysplasia congenita (35 variants)
- COL2A1-related condition (34 variants)
- Achondrogenesis type II (31 variants)
- 16 conditions (23 variants)
- Spondyloperipheral dysplasia (20 variants)
- Kniest dysplasia (14 variants)
- Spondyloepimetaphyseal dysplasia, Strudwick type (13 variants)
- Stickler syndrome, type I, nonsyndromic ocular (12 variants)
- Spondyloepiphyseal dysplasia, Stanescu type (9 variants)
- Platyspondylic dysplasia, Torrance type (7 variants)
- Avascular necrosis of femoral head, primary, 1 (5 variants)
- Type 2 collagenopathy (5 variants)
- COL2A1-related disorders (5 variants)
- Retinal dystrophy (5 variants)
- See cases (4 variants)
- 14 conditions (4 variants)
- MASS syndrome (3 variants)
- Spondylometaphyseal dysplasia - Sutcliffe type (3 variants)
- Autosomal dominant rhegmatogenous retinal detachment (2 variants)
- Intellectual disability (2 variants)
- COL2A1-related skeletal dysplasia (2 variants)
- Otospondylomegaepiphyseal dysplasia, autosomal dominant (2 variants)
- Stickler Syndrome, Dominant (2 variants)
- Czech dysplasia, metatarsal type (2 variants)
- Stickler syndrome (2 variants)
- Multiple epiphyseal dysplasia, Beighton type (2 variants)
- 8 conditions (2 variants)
- Namaqualand hip dysplasia (2 variants)
- Hearing impairment (2 variants)
- 6 conditions (2 variants)
- Orofacial cleft 1 (1 variants)
- Abnormality of the skeletal system (1 variants)
- Skeletal dysplasia (1 variants)
- Marfan syndrome (1 variants)
- Absent vertebral body mineralization;Short ribs (1 variants)
- Hereditary breast ovarian cancer syndrome (1 variants)
- Mendelian syndromes with cleft lip/palate (1 variants)
- COL2A1-Related Disorder (1 variants)
- Kniest dysplasia;Spondyloepimetaphyseal dysplasia, Strudwick type (1 variants)
- Retinitis pigmentosa (1 variants)
- Myopia (1 variants)
- Narrow chest;Disproportionate short-limb short stature (1 variants)
- Maffucci syndrome (1 variants)
- 9 conditions (1 variants)
- Heart, malformation of;Micrognathia (1 variants)
- Legg-Calve-Perthes disease (1 variants)
- Acetabular dysplasia (1 variants)
- Otospondylomegaepiphyseal dysplasia, autosomal recessive (1 variants)
- Stargardt disease (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL2A1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 275 | 13 | 300 | ||
| missense | 104 | 226 | 438 | 76 | 27 | 871 |
| nonsense | 64 | 71 | ||||
| start loss | 2 | |||||
| frameshift | 180 | 16 | 198 | |||
| inframe indel | 20 | 34 | ||||
| splice donor/acceptor (+/-2bp) | 64 | 73 | 142 | |||
| splice region ? | 14 | 69 | 90 | 6 | 179 | |
| non coding ? | 19 | 292 | 138 | 450 | ||
| Total | 420 | 344 | 483 | 643 | 178 |
Highest pathogenic variant AF is 0.00000657
Variants in COL2A1
This is a list of pathogenic ClinVar variants found in the COL2A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-47973001-T-C | Type II Collagenopathies • Stickler syndrome type 1 | Uncertain significance (Jan 12, 2018) | ||
| 12-47973034-C-G | Stickler syndrome type 1 • Type II Collagenopathies | Uncertain significance (Mar 30, 2018) | ||
| 12-47973076-C-T | Stickler syndrome type 1 • Type II Collagenopathies | Uncertain significance (Mar 02, 2018) | ||
| 12-47973102-C-T | Stickler syndrome type 1 • Type II Collagenopathies | Conflicting classifications of pathogenicity (Jan 01, 2023) | ||
| 12-47973112-G-A | Stickler syndrome type 1 • Type II Collagenopathies | Benign (Jul 27, 2018) | ||
| 12-47973172-G-A | Likely benign (Apr 30, 2019) | |||
| 12-47973249-G-T | Type II Collagenopathies • Stickler syndrome type 1 | Uncertain significance (Jan 12, 2018) | ||
| 12-47973271-G-A | Type II Collagenopathies • Stickler syndrome type 1 | Benign (Jun 14, 2018) | ||
| 12-47973276-G-A | Stickler syndrome type 1 • Type II Collagenopathies | Uncertain significance (Jan 12, 2018) | ||
| 12-47973287-G-C | Stickler syndrome type 1 • Type II Collagenopathies | Uncertain significance (Jan 13, 2018) | ||
| 12-47973379-G-A | Stickler syndrome type 1 • Type II Collagenopathies | Likely benign (Jun 14, 2018) | ||
| 12-47973403-G-A | Type II Collagenopathies • Stickler syndrome type 1 • not specified • Connective tissue disorder | Benign (Nov 22, 2023) | ||
| 12-47973407-T-A | Stickler syndrome, type I, nonsyndromic ocular | Uncertain significance (Sep 01, 2022) | ||
| 12-47973408-T-G | Uncertain significance (May 19, 2023) | |||
| 12-47973409-A-C | Uncertain significance (May 27, 2023) | |||
| 12-47973409-A-G | Uncertain significance (Aug 02, 2022) | |||
| 12-47973409-A-T | Uncertain significance (Dec 09, 2023) | |||
| 12-47973410-CAAG-C | Likely pathogenic (Oct 17, 2022) | |||
| 12-47973412-A-T | Uncertain significance (Apr 12, 2023) | |||
| 12-47973418-A-G | Spondyloepiphyseal dysplasia congenita | Conflicting classifications of pathogenicity (Sep 25, 2023) | ||
| 12-47973420-ACCGG-A | Pathogenic (Feb 05, 2015) | |||
| 12-47973422-C-T | not specified • Connective tissue disorder | Benign (Jan 29, 2024) | ||
| 12-47973423-G-A | Type II Collagenopathies • Stickler syndrome type 1 | Conflicting classifications of pathogenicity (Jan 11, 2024) | ||
| 12-47973427-C-T | Inborn genetic diseases | Uncertain significance (May 26, 2023) | ||
| 12-47973427-C-CT | Pathogenic (Nov 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COL2A1 | protein_coding | protein_coding | ENST00000380518 | 54 | 31522 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 1.55e-10 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.29 | 604 | 879 | 0.687 | 0.0000538 | 9191 |
| Missense in Polyphen | 25 | 79.73 | 0.31356 | 793 | ||
| Synonymous | -1.67 | 358 | 320 | 1.12 | 0.0000215 | 3311 |
| Loss of Function | 8.12 | 6 | 88.4 | 0.0679 | 0.00000493 | 1026 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000185 | 0.000181 |
| Ashkenazi Jewish | 0.000201 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000355 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces.;
- Disease
- DISEASE: Spondyloepiphyseal dysplasia congenital type (SEDC) [MIM:183900]: Disorder characterized by disproportionate short stature and pleiotropic involvement of the skeletal and ocular systems. {ECO:0000269|PubMed:10678662, ECO:0000269|PubMed:11746045, ECO:0000269|PubMed:2339128, ECO:0000269|PubMed:2543071, ECO:0000269|PubMed:7757086, ECO:0000269|PubMed:8019561, ECO:0000269|PubMed:8325895, ECO:0000269|PubMed:8423604}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spondyloepiphyseal dysplasia, Stanescu type (SEDSTN) [MIM:616583]: An autosomal dominant spondyloepiphyseal dysplasia characterized by glycoproteins accumulation in chondrocytes. Clinical features include progressive joint contractures, premature degenerative joint disease particularly in the knee, hip and finger joints, and osseous distention of the metaphyseal ends of the phalanges causing swolling of interphalangeal joints of the hands. Radiological features include generalized platyspondyly, hypoplastic pelvis, epiphyseal flattening with metaphyseal splaying of the long bones, and enlarged phalangeal epimetaphyses of the hands. {ECO:0000269|PubMed:26183434}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spondyloepimetaphyseal dysplasia, Strudwick type (SEMDSTWK) [MIM:184250]: A bone disease characterized by disproportionate short stature from birth, with a very short trunk and shortened limbs, and skeletal abnormalities including lordosis, scoliosis, flattened vertebrae, pectus carinatum, coxa vara, clubfoot, and abnormal epiphyses or metaphyses. A distinctive radiographic feature is irregular sclerotic changes, described as dappled in the metaphyses of the long bones. {ECO:0000269|PubMed:16088915, ECO:0000269|PubMed:7550321, ECO:0000269|Ref.39}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Achondrogenesis 2 (ACG2) [MIM:200610]: An autosomal dominant disease characterized by the absence of ossification in the vertebral column, sacrum and pubic bones. {ECO:0000269|PubMed:10745044, ECO:0000269|PubMed:10797431, ECO:0000269|PubMed:15054848, ECO:0000269|PubMed:17994563, ECO:0000269|PubMed:2572591, ECO:0000269|PubMed:7757081, ECO:0000269|PubMed:7757086, ECO:0000269|PubMed:7829510}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Legg-Calve-Perthes disease (LCPD) [MIM:150600]: Characterized by loss of circulation to the femoral head, resulting in avascular necrosis in a growing child. Clinical pictures of the disease vary, depending on the phase of disease progression through ischemia, revascularization, fracture and collapse, and repair and remodeling of the bone. {ECO:0000269|PubMed:17394019}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Kniest dysplasia (KD) [MIM:156550]: Moderately severe chondrodysplasia phenotype that results from mutations in the COL2A1 gene. Characteristics of the disorder include a short trunk and extremities, mid-face hypoplasia, cleft palate, myopia, retinal detachment, and hearing loss. {ECO:0000269|PubMed:7874117, ECO:0000269|PubMed:8863156}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Avascular necrosis of femoral head, primary, 1 (ANFH1) [MIM:608805]: A disease characterized by mechanical failure of the subchondral bone, and degeneration of the hip joint. It usually leads to destruction of the hip joint in the third to fifth decade of life. The clinical manifestations, such as pain on exertion, a limping gait, and a discrepancy in leg length, cause considerable disability. ANFH1 inheritance is autosomal dominant. {ECO:0000269|PubMed:15930420, ECO:0000269|PubMed:21671384}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteoarthritis with mild chondrodysplasia (OSCDP) [MIM:604864]: Osteoarthritis is a common disease that produces joint pain and stiffness together with radiologic evidence of progressive degeneration of joint cartilage. {ECO:0000269|PubMed:1975693, ECO:0000269|PubMed:1985108, ECO:0000269|PubMed:7757086, ECO:0000269|PubMed:8507190}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Platyspondylic lethal skeletal dysplasia Torrance type (PLSD-T) [MIM:151210]: Platyspondylic lethal skeletal dysplasias (PLSDs) are a heterogeneous group of chondrodysplasias characterized by severe platyspondyly and limb shortening. PLSD-T is characterized by varying platyspondyly, short ribs with anterior cupping, hypoplasia of the lower ilia with broad ischial and pubic bones, and shortening of the tubular bones with splayed and cupped metaphyses. Histology of the growth plate typically shows focal hypercellularity with slightly enlarged chondrocytes in the resting cartilage and relatively well-preserved columnar formation and ossification at the chondro-osseous junction. PLSD-T is generally a perinatally lethal disease, but a few long-term survivors have been reported. {ECO:0000269|PubMed:10745044, ECO:0000269|PubMed:14729840, ECO:0000269|PubMed:15643621}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple epiphyseal dysplasia with myopia and conductive deafness (EDMMD) [MIM:132450]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. EDMMD is an autosomal dominant disorder characterized by epiphyseal dysplasia associated with progressive myopia, retinal thinning, crenated cataracts, conductive deafness. {ECO:0000269|PubMed:9800905}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spondyloperipheral dysplasia (SPD) [MIM:271700]: SPD patients manifest short stature, midface hypoplasia, sensorineural hearing loss, spondyloepiphyseal dysplasia, platyspondyly and brachydactyly. {ECO:0000269|PubMed:15316962}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Stickler syndrome 1 (STL1) [MIM:108300]: An autosomal dominant form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Pierre Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable. {ECO:0000269|PubMed:11007540, ECO:0000269|PubMed:20513134, ECO:0000269|PubMed:7977371}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Stickler syndrome 1 non-syndromic ocular (STL1O) [MIM:609508]: An autosomal dominant form of Stickler syndrome characterized by the ocular signs typically seen in Stickler syndrome type 1 such as cataract, myopia, retinal detachment. Systemic features of premature osteoarthritis, cleft palate, hearing impairment, and craniofacial abnormalities are either absent or very mild. {ECO:0000269|PubMed:16752401, ECO:0000269|PubMed:17721977, ECO:0000269|PubMed:8317498}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Rhegmatogenous retinal detachment autosomal dominant (DRRD) [MIM:609508]: A eye disease that most frequently results from a break or tear in the retina that allows fluid from the vitreous humor to enter the potential space beneath the retina. It is often associated with pathologic myopia and in most cases leads to visual impairment or blindness if untreated. {ECO:0000269|PubMed:11007540, ECO:0000269|PubMed:15671297}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Czech dysplasia (CZECHD) [MIM:609162]: A skeletal dysplasia characterized by early-onset, progressive pseudorheumatoid arthritis, platyspondyly, and short third and fourth toes. {ECO:0000269|PubMed:18553548, ECO:0000269|PubMed:19764028, ECO:0000269|PubMed:7757086, ECO:0000269|PubMed:8244341}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Neural Crest Differentiation;Spinal Cord Injury;Focal Adhesion;Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Endochondral Ossification;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;Integrin;Beta1 integrin cell surface interactions;Syndecan-1-mediated signaling events;Integrins in angiogenesis
(Consensus)
Recessive Scores
- pRec
- 0.927
Intolerance Scores
- loftool
- 0.00641
- rvis_EVS
- -1.8
- rvis_percentile_EVS
- 2.21
Haploinsufficiency Scores
- pHI
- 0.966
- hipred
- Y
- hipred_score
- 0.714
- ghis
- 0.419
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.700
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Col2a1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype;
Zebrafish Information Network
- Gene name
- col2a1a
- Affected structure
- vertebra
- Phenotype tag
- abnormal
- Phenotype quality
- fused with
Gene ontology
- Biological process
- skeletal system development;cartilage condensation;tissue homeostasis;endochondral ossification;chondrocyte differentiation;heart morphogenesis;proteoglycan metabolic process;central nervous system development;visual perception;sensory perception of sound;regulation of gene expression;extracellular matrix organization;collagen fibril organization;notochord development;inner ear morphogenesis;regulation of immune response;cartilage development;roof of mouth development;limb bud formation;embryonic skeletal joint morphogenesis;cartilage development involved in endochondral bone morphogenesis;otic vesicle development;cellular response to BMP stimulus;anterior head development;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- extracellular region;collagen trimer;collagen type II trimer;basement membrane;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
- Molecular function
- extracellular matrix structural constituent;extracellular matrix structural constituent conferring tensile strength;MHC class II protein binding;identical protein binding;proteoglycan binding;metal ion binding;platelet-derived growth factor binding