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COL1A2

collagen type I alpha 2 chain, the group of Collagens

Basic information

Region (hg38): 7:94394894-94431227

Previous symbols: [ "OI4" ]

Links

ENSG00000164692NCBI:1278OMIM:120160HGNC:2198Uniprot:P08123AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ehlers-danlos syndrome, arthrochalasia type, 2 (Strong), mode of inheritance: AD
  • Ehlers-Danlos syndrome, cardiac valvular type (Strong), mode of inheritance: AR
  • ehlers-danlos syndrome, arthrochalasia type, 2 (Strong), mode of inheritance: AD
  • Ehlers-Danlos syndrome, cardiac valvular type (Strong), mode of inheritance: AR
  • Ehlers-Danlos syndrome, arthrochalasia type (Supportive), mode of inheritance: AD
  • osteogenesis imperfecta type 1 (Supportive), mode of inheritance: AD
  • osteogenesis imperfecta type 2 (Supportive), mode of inheritance: AD
  • osteogenesis imperfecta type 3 (Supportive), mode of inheritance: AD
  • osteogenesis imperfecta type 4 (Supportive), mode of inheritance: AD
  • Ehlers-Danlos syndrome, cardiac valvular type (Supportive), mode of inheritance: AR
  • Ehlers-Danlos/osteogenesis imperfecta syndrome (Supportive), mode of inheritance: AD
  • high bone mass osteogenesis imperfecta (Supportive), mode of inheritance: AD
  • ehlers-danlos syndrome, arthrochalasia type, 2 (Definitive), mode of inheritance: AD
  • combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2 (Moderate), mode of inheritance: AD
  • Ehlers-Danlos syndrome, cardiac valvular type (Definitive), mode of inheritance: AR
  • Ehlers-Danlos syndrome, arthrochalasia type (Strong), mode of inheritance: AR
  • osteogenesis imperfecta type 3 (Strong), mode of inheritance: AD
  • ehlers-danlos syndrome, arthrochalasia type, 2 (Strong), mode of inheritance: AD
  • osteogenesis imperfecta type 4 (Definitive), mode of inheritance: AD
  • osteogenesis imperfecta type 2 (Definitive), mode of inheritance: AD
  • osteogenesis imperfecta type 1 (Definitive), mode of inheritance: AD
  • osteogenesis imperfecta type 3 (Definitive), mode of inheritance: AD
  • Ehlers-Danlos syndrome, arthrochalasia type (Definitive), mode of inheritance: AD
  • Ehlers-Danlos syndrome, cardiac valvular type (Definitive), mode of inheritance: AR
  • combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2; Ehlers-Danlos syndrome, cardiac valvular formAD/ARCardiovascularEhlers-Danlos syndrome, cardiac valvular form may be difficult to recognize, and cardiac manifestations, which can include arrhythmias may benefit from early (including surgical) interventions; Some individuals may also have arterial/vascular fragility, and awareness may allow appropriate precautions and prompt management of sequelae; In In Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1, cardiovascular manifestations (eg, aortic dilatation, vascular fragility) have been described, and awareness may allow surveillance and managementAudiologic/Otolaryngologic; Cardiovascular; Dermatologic; Musculoskeletal; Ophthalmologic4742738; 6773953; 3940669; 2952379; 3621666; 3680255; 2454224; 2897363; 2777808; 1712342; 1301191; 1577745; 7916744; 8071956; 8950681; 9386671; 9295084; 9099837; 9753709; 10843163; 11760017; 11970931; 12417561; 12417568; 12629073; 12728084; 15241796; 15077201; 16778601; 16816023; 16434452; 17217883; 18996919; 19208385; 20087402; 21667357; 22206639; 22791419; 22795120; 23118688; 23692737

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL1A2 gene.

  • not provided (591 variants)
  • Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 (548 variants)
  • Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I (460 variants)
  • Cardiovascular phenotype (278 variants)
  • Osteogenesis imperfecta (184 variants)
  • Ehlers-danlos syndrome, arthrochalasia type, 2 (120 variants)
  • not specified (91 variants)
  • Ehlers-Danlos syndrome (49 variants)
  • Osteogenesis imperfecta with normal sclerae, dominant form (40 variants)
  • Osteogenesis imperfecta, recessive perinatal lethal (38 variants)
  • Osteogenesis imperfecta type III (27 variants)
  • Connective tissue disorder (24 variants)
  • COL1A2-related condition (17 variants)
  • Osteogenesis imperfecta type I (14 variants)
  • 7 conditions (12 variants)
  • Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2 (12 variants)
  • Inborn genetic diseases (10 variants)
  • 6 conditions (8 variants)
  • Ehlers-Danlos syndrome, classic type (7 variants)
  • Ehlers-Danlos syndrome, classic type;Osteogenesis imperfecta type I (7 variants)
  • Ehlers-Danlos syndrome, cardiac valvular type (6 variants)
  • See cases (6 variants)
  • Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type (5 variants)
  • COL1A2-Related Disorder (5 variants)
  • Ehlers-Danlos syndrome, arthrochalasis type (4 variants)
  • COL1A2-Related Disorders (3 variants)
  • Abnormality of the skeletal system (3 variants)
  • Dentinogenesis imperfecta (3 variants)
  • Osteogenesis imperfecta with normal sclerae, dominant form;Osteogenesis imperfecta, recessive perinatal lethal;Osteogenesis imperfecta type III (3 variants)
  • Osteogenesis Imperfecta, Dominant (3 variants)
  • Ehlers-danlos syndrome, arthrochalasia type, 2;Ehlers-Danlos syndrome, cardiac valvular type;Osteogenesis imperfecta (2 variants)
  • Postmenopausal osteoporosis (2 variants)
  • Osteogenesis imperfecta;Ehlers-Danlos syndrome, cardiac valvular type;Ehlers-Danlos syndrome, arthrochalasis type (2 variants)
  • Marfan syndrome, atypical (1 variants)
  • Ehlers-danlos syndrome, arthrochalasia type, 2;Osteogenesis imperfecta with normal sclerae, dominant form;Osteogenesis imperfecta, recessive perinatal lethal;Osteogenesis imperfecta type III;Ehlers-Danlos syndrome, cardiac valvular type (1 variants)
  • Skeletal dysplasia (1 variants)
  • Bruck syndrome 1 (1 variants)
  • Collagen type 1 disorder (1 variants)
  • Rare disease with thoracic aortic aneurysm and aortic dissection (1 variants)
  • Predisposition to dissection (1 variants)
  • Osteogenesis imperfecta, recessive perinatal lethal;Ehlers-Danlos syndrome, arthrochalasis type;Ehlers-Danlos syndrome, cardiac valvular type (1 variants)
  • - (1 variants)
  • Osteogenesis imperfecta with normal sclerae, dominant form;Osteogenesis imperfecta type III (1 variants)
  • Multiple prenatal fractures;Skeletal dysplasia (1 variants)
  • Osteogenesis imperfecta, mild (1 variants)
  • Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, cardiac valvular type;Ehlers-danlos syndrome, arthrochalasia type, 2 (1 variants)
  • Increased susceptibility to fractures (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL1A2 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
19
clinvar
245
clinvar
5
clinvar
269
missense
181
clinvar
169
clinvar
395
clinvar
15
clinvar
3
clinvar
763
nonsense
3
clinvar
1
clinvar
4
clinvar
8
start loss
0
frameshift
12
clinvar
10
clinvar
3
clinvar
25
inframe indel
2
clinvar
9
clinvar
10
clinvar
21
splice donor/acceptor (+/-2bp)
23
clinvar
23
clinvar
46
splice region
8
4
51
59
6
128
non coding
26
clinvar
200
clinvar
90
clinvar
316
Total 221 212 457 460 98

Highest pathogenic variant AF is 0.0000132

Variants in COL1A2

This is a list of pathogenic ClinVar variants found in the COL1A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
7-94394945-C-T Osteogenesis imperfecta • Ehlers-danlos syndrome, arthrochalasia type, 2 Uncertain significance (Jan 13, 2018)360941
7-94395027-T-C Likely benign (Apr 01, 2023)2571282
7-94395032-A-T Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Uncertain significance (Jun 12, 2023)2928734
7-94395053-C-T Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Uncertain significance (Dec 18, 2022)2922796
7-94395060-T-G Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Uncertain significance (Dec 30, 2023)2931667
7-94395063-T-C Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Uncertain significance (Apr 12, 2022)2159411
7-94395067-G-C Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Likely benign (Dec 22, 2018)799317
7-94395079-C-T Connective tissue disorder • Ehlers-danlos syndrome, arthrochalasia type, 2 • Osteogenesis imperfecta • Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I • Cardiovascular phenotype Benign/Likely benign (Sep 03, 2023)456841
7-94395083-T-C 6 conditions • Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I Uncertain significance (Sep 27, 2023)526891
7-94395083-T-G Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I • COL1A2-related disorder Conflicting classifications of pathogenicity (Nov 03, 2023)456832
7-94395088-A-G Cardiovascular phenotype Likely benign (Apr 26, 2019)1749730
7-94395089-G-A Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Uncertain significance (May 23, 2023)2183136
7-94395091-A-C Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 • Cardiovascular phenotype Likely benign (Nov 01, 2022)762753
7-94395098-C-T Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2;Ehlers-danlos syndrome, arthrochalasia type, 2;Osteogenesis imperfecta, perinatal lethal;Ehlers-Danlos syndrome, cardiac valvular type;Osteogenesis imperfecta with normal sclerae, dominant form not provided (-)3064039
7-94395100-A-G Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 • Cardiovascular phenotype Conflicting classifications of pathogenicity (Dec 19, 2023)1418847
7-94395109-C-A Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Likely benign (Oct 15, 2023)2952503
7-94395109-C-T Ehlers-Danlos syndrome, classic type, 1;Osteogenesis imperfecta type I Likely benign (Jul 12, 2022)456842
7-94395110-C-T not specified Likely benign (Nov 15, 2023)2682526
7-94395119-G-A Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type, 1 Likely benign (Aug 28, 2023)2951395
7-94395619-A-G Benign (Aug 30, 2018)1239407
7-94395760-G-T Likely benign (Aug 12, 2018)1196315
7-94395775-A-G Likely benign (Jun 14, 2018)672687
7-94395818-A-G Ehlers-Danlos syndrome, cardiac valvular type Pathogenic (May 01, 2004)17276
7-94395819-TAA-T Benign/Likely benign (Jul 21, 2021)671158
7-94395905-T-C Likely benign (Jun 14, 2018)672688

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COL1A2protein_codingprotein_codingENST00000297268 5236672
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000001241257001471257480.000191
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.156418130.7880.00004748521
Missense in Polyphen3262.3850.51294621
Synonymous-1.442972671.110.00001603088
Loss of Function7.22977.60.1160.00000401939

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002610.000261
Ashkenazi Jewish0.0001990.000198
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00008300.0000791
Middle Eastern0.0001090.000109
South Asian0.0008820.000850
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen).;
Disease
DISEASE: Ehlers-Danlos syndrome, arthrochalasia type, 2 (EDSARTH2) [MIM:617821]: A form of Ehlers-Danlos syndrome, a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDSARTH2 is an autosomal dominant condition characterized by frequent congenital hip dislocation and extreme joint laxity with recurrent joint subluxations and minimal skin involvement. {ECO:0000269|PubMed:1577745, ECO:0000269|PubMed:2394758, ECO:0000269|PubMed:3680255}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteogenesis imperfecta 1 (OI1) [MIM:166200]: An autosomal dominant form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI1 is a non-deforming form with normal height or mild short stature, and no dentinogenesis imperfecta. {ECO:0000269|PubMed:16705691, ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:1990009, ECO:0000269|PubMed:8456807, ECO:0000269|PubMed:8829649}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteogenesis imperfecta 2 (OI2) [MIM:166210]: An autosomal dominant form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI2 is characterized by bone fragility, with many perinatal fractures, severe bowing of long bones, undermineralization, and death in the perinatal period due to respiratory insufficiency. {ECO:0000269|PubMed:10627137, ECO:0000269|PubMed:1284475, ECO:0000269|PubMed:1339453, ECO:0000269|PubMed:1385413, ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:16879195, ECO:0000269|PubMed:1874719, ECO:0000269|PubMed:18996919, ECO:0000269|PubMed:2777764, ECO:0000269|PubMed:2914942, ECO:0000269|PubMed:7693712, ECO:0000269|PubMed:7891382, ECO:0000269|PubMed:7906591, ECO:0000269|PubMed:7959683, ECO:0000269|PubMed:8182080, ECO:0000269|Ref.34}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ehlers-Danlos syndrome, cardiac valvular type (EDSCV) [MIM:225320]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. EDSCV is an autosomal recessive disease characterized by mitral valve prolapse and insufficiency, mitral regurgitation, and aortic insufficiency, in addition to joint laxity, skin hyperextensibility and friability, and abnormal scar formation. {ECO:0000269|PubMed:16816023}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteogenesis imperfecta 3 (OI3) [MIM:259420]: An autosomal dominant form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI3 is characterized by progressively deforming bones, very short stature, a triangular face, severe scoliosis, grayish sclera and dentinogenesis imperfecta. {ECO:0000269|PubMed:10408781, ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:16879195, ECO:0000269|PubMed:1990009, ECO:0000269|PubMed:7520724, ECO:0000269|PubMed:7720740, ECO:0000269|PubMed:7749416, ECO:0000269|PubMed:7860070, ECO:0000269|PubMed:7881420, ECO:0000269|PubMed:8081394, ECO:0000269|PubMed:8444468, ECO:0000269|PubMed:8456807, ECO:0000269|PubMed:8723681, ECO:0000269|PubMed:8800927, ECO:0000269|PubMed:8829649}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteogenesis imperfecta 4 (OI4) [MIM:166220]: An autosomal dominant form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI4 is characterized by moderately short stature, mild to moderate scoliosis, grayish or white sclera and dentinogenesis imperfecta. {ECO:0000269|PubMed:1642148, ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:16879195, ECO:0000269|PubMed:2052622, ECO:0000269|PubMed:2064612, ECO:0000269|PubMed:2897363, ECO:0000269|PubMed:7693712, ECO:0000269|PubMed:8094076, ECO:0000269|PubMed:8401517, ECO:0000269|PubMed:8800927}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving COL1A2 may be a cause of lipoblastomas, which are benign tumors resulting from transformation of adipocytes, usually diagnosed in children. Translocation t(7;8)(p22;q13) with PLAG1.;
Pathway
PI3K-Akt signaling pathway - Homo sapiens (human);Platelet activation - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;miR-targeted genes in muscle cell - TarBase;miRNA targets in ECM and membrane receptors;Focal Adhesion;TGF-beta Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Protein alkylation leading to liver fibrosis;Interleukin-4 and 13 signaling;PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;Vesicle-mediated transport;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;Beta3 integrin cell surface interactions;Integrin;VEGFR3 signaling in lymphatic endothelium;C-MYB transcription factor network;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors;Validated targets of C-MYC transcriptional repression;Beta1 integrin cell surface interactions;AP-1 transcription factor network;Syndecan-1-mediated signaling events;IL4-mediated signaling events;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Regulation of nuclear SMAD2/3 signaling;Endothelins;Integrins in angiogenesis (Consensus)

Intolerance Scores

loftool
0.00710
rvis_EVS
-1.14
rvis_percentile_EVS
6.36

Haploinsufficiency Scores

pHI
0.999
hipred
Y
hipred_score
0.822
ghis
0.640

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.170

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Col1a2
Phenotype
homeostasis/metabolism phenotype; muscle 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; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
col1a2
Affected structure
vertebra
Phenotype tag
abnormal
Phenotype quality
deformed

Gene ontology

Biological process
skeletal system development;blood vessel development;transforming growth factor beta receptor signaling pathway;Rho protein signal transduction;blood coagulation;regulation of blood pressure;cytokine-mediated signaling pathway;platelet activation;extracellular matrix organization;collagen fibril organization;odontogenesis;skin morphogenesis;regulation of immune response;leukocyte migration;protein heterotrimerization;cellular response to amino acid stimulus
Cellular component
extracellular region;collagen type I trimer;extracellular space;endoplasmic reticulum;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix;extracellular exosome
Molecular function
protease binding;extracellular matrix structural constituent;protein binding;extracellular matrix structural constituent conferring tensile strength;protein binding, bridging;identical protein binding;SMAD binding;metal ion binding;platelet-derived growth factor binding