COL1A1

collagen type I alpha 1 chain, the group of Collagens

Basic information

Region (hg38): 17:50184100-50201632

Links

ENSG00000108821 ∙ NCBI:1277 ∙ OMIM:120150 ∙ HGNC:2197 ∙ Uniprot:P02452 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ehlers-Danlos syndrome, arthrochalasia type (Definitive), mode of inheritance: AD
• Caffey disease (Definitive), mode of inheritance: AD
• osteogenesis imperfecta type 2 (Definitive), mode of inheritance: AD
• Ehlers-Danlos syndrome, arthrochalasia type (Strong), mode of inheritance: AD
• Ehlers-Danlos syndrome, arthrochalasia type (Strong), mode of inheritance: AD
• osteogenesis imperfecta type 1 (Definitive), mode of inheritance: AD
• Caffey disease (Supportive), mode of inheritance: AD
• Ehlers-Danlos syndrome, classic type (Supportive), mode of inheritance: AD
• 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/osteogenesis imperfecta syndrome (Supportive), mode of inheritance: AD
• high bone mass osteogenesis imperfecta (Supportive), mode of inheritance: AD
• Caffey disease (Strong), mode of inheritance: AD
• combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1 (Moderate), mode of inheritance: AD
• Caffey disease (Moderate), mode of inheritance: AD
• osteogenesis imperfecta type 3 (Definitive), mode of inheritance: AD
• Ehlers-Danlos syndrome, arthrochalasia type (Strong), mode of inheritance: AD
• osteogenesis imperfecta type 3 (Strong), mode of inheritance: AD
• osteogenesis imperfecta type 2 (Definitive), mode of inheritance: AD
• Caffey disease (Definitive), mode of inheritance: AD
• Ehlers-Danlos syndrome, classic type, 1 (Moderate), mode of inheritance: AD
• osteogenesis imperfecta type 1 (Definitive), mode of inheritance: AD
• osteogenesis imperfecta type 3 (Definitive), mode of inheritance: AD
• combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1 (Definitive), mode of inheritance: AD
• osteogenesis imperfecta type 4 (Definitive), mode of inheritance: AD
• Ehlers-Danlos syndrome, arthrochalasia type (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, classic type, 1; Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1	AD	Cardiovascular; Obstetric	Individuals with Ehlers-Danlos syndrome, classic type, 1; ay have aortic root dilatation (as well as arterial/vascular fragility), but the natural history is unclear, and many not commonly progress, though yearly surveillance with echocardiogram when aortic dilatation or mitral valve prolapse is peresent has been recommended; Precautions in pregnancy may be beneficial; In Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1, cardiovascular manifestations such as aortic root dilatation have been described, and awareness may allow surveillance and management	Audiologic/Otolaryngologic; Cardiovascular; Dermatologic; Musculoskeletal; Obstetric; Ophthalmologic	1146889; 1054840; 6304100; 3001313; 3016737; 3082886; 3722186; 3940669; 3108247; 3667599; 3403550; 3341380; 2745420; 2511192; 2794057; 2767050; 2777808 ; 2309707; 2121988; 2339700; 2295701; 1867198; 2037280; 1301191; 1353940; 8408653; 7789952; 9007315; 8757037; 8723681; 8613526; 8910493; 9386671; 9295084; 9067755; 9101290; 9143923; 9753709; 9753715; 10417276; 10739762; 10843163; 11286507; 11760017; 11668615; 11970931; 11704682; 12417561; 12417568; 12524541; 12629073; 12728084; 15024692; 15241796; 15728585; 15864348; 16272059; 16291701; 16434452; 16778601; 17078022; 17211858; 17217883; 17309652; 18409203; 18553566; 18996919; 19929435; 20087402; 21667357; 22206639; 22565191; 22791419; 22795108; 22855962; 22987783; 23072183; 23118688; 23682531; 23692737; 28261977

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL1A1 gene.

• Osteogenesis imperfecta type I (1763 variants)
• not provided (725 variants)
• Cardiovascular phenotype (335 variants)
• Osteogenesis imperfecta (287 variants)
• Infantile cortical hyperostosis (170 variants)
• Ehlers-Danlos syndrome, arthrochalasis type (148 variants)
• not specified (135 variants)
• Ehlers-Danlos syndrome (84 variants)
• Osteogenesis imperfecta with normal sclerae, dominant form (49 variants)
• COL1A1-related condition (45 variants)
• Osteogenesis imperfecta, recessive perinatal lethal (38 variants)
• Osteogenesis imperfecta type III (30 variants)
• 8 conditions (28 variants)
• Ehlers-Danlos syndrome type 7A (22 variants)
• Osteogenesis Imperfecta, Dominant (22 variants)
• Connective tissue disorder (21 variants)
• 7 conditions (11 variants)
• Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1 (10 variants)
• See cases (9 variants)
• Inborn genetic diseases (5 variants)
• Abnormality of the skeletal system (3 variants)
• Familial thoracic aortic aneurysm and aortic dissection (2 variants)
• Ehlers-Danlos syndrome, arthrochalasis type;Osteogenesis imperfecta (2 variants)
• - (2 variants)
• Postmenopausal osteoporosis (2 variants)
• Osteogenesis imperfecta type 1, mild (2 variants)
• Wiedemann-Rautenstrauch-like progeroid syndrome (1 variants)
• Congenital heart disease (1 variants)
• Osteoporosis (1 variants)
• Ehlers-Danlos syndrome, classic type (1 variants)
• Keratoconus (1 variants)
• Osteogenesis imperfecta with normal sclerae, dominant form;Osteogenesis imperfecta type I;Osteogenesis imperfecta type III;Osteogenesis imperfecta, recessive perinatal lethal (1 variants)
• Infantile cortical hyperostosis;Ehlers-danlos syndrome, arthrochalasia type, 2;Osteogenesis imperfecta (1 variants)
• Phenylketonuria (1 variants)
• Abnormal bleeding (1 variants)
• Primary dilated cardiomyopathy (1 variants)
• COL1A1-related osteogenesis imperfecta (1 variants)
• Abnormality of connective tissue (1 variants)
• Ehlers-Danlos syndrome, classic type, 1 (1 variants)
• COL1A1-related disease (1 variants)
• 27 conditions (1 variants)
• Ehlers-danlos syndrome, arthrochalasia type, 2 (1 variants)
• Osteogenesis imperfecta;Ehlers-Danlos syndrome, classic type;Ehlers-Danlos syndrome, arthrochalasis type;Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1 (1 variants)
• Hypertrophic cardiomyopathy (1 variants)
• Bruising susceptibility;Fragile skin;Joint hypermobility (1 variants)
• Osteogenesis imperfecta type III;Osteogenesis imperfecta with normal sclerae, dominant form (1 variants)
• Abnormality of bone mineral density (1 variants)
• Osteogenesis imperfecta;Infantile cortical hyperostosis;Ehlers-Danlos syndrome, cardiac valvular type;Ehlers-Danlos syndrome, arthrochalasis type (1 variants)
• Multiple epiphyseal dysplasia type 1 (1 variants)
• Reduced bone mineral density;Joint hypermobility (1 variants)
• Infantile cortical hyperostosis;Osteogenesis imperfecta type I;Ehlers-Danlos syndrome, classic type;Ehlers-Danlos syndrome, arthrochalasis type (1 variants)
• Recurrent fractures;Dentinogenesis imperfecta (1 variants)
• Abnormal bone structure (1 variants)
• Osteopenia;Blue sclerae;Increased susceptibility to fractures (1 variants)
• Infantile cortical hyperostosis;Ehlers-Danlos syndrome, arthrochalasis type;Osteogenesis imperfecta (1 variants)
• Infantile cortical hyperostosis;Osteogenesis imperfecta;Ehlers-Danlos syndrome, arthrochalasis type (1 variants)
• 6 conditions (1 variants)
• Recurrent fractures;Blue sclerae (1 variants)
• Malignant tumor of prostate (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL1A1 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			15	304	8	327
missense	150	152	351	63	15	731
nonsense	89	11				100
start loss	6					6
frameshift	286	44	1			331
inframe indel	6	8	12			26
splice donor/acceptor (+/-2bp)	138	38	7			183
splice region	6	7	77	62	6	158
non coding	2	3	63	238	71	377
Total	677	256	449	605	94

Highest pathogenic variant AF is 0.00000660

Variants in COL1A1

This is a list of pathogenic ClinVar variants found in the COL1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50184114-CACAT-C		Infantile cortical hyperostosis • Ehlers-Danlos syndrome type 7A • Osteogenesis Imperfecta, Dominant	Uncertain significance (Jun 14, 2016)
17-50184178-T-C		Ehlers-Danlos syndrome, arthrochalasia type • Infantile cortical hyperostosis • Osteogenesis imperfecta	Uncertain significance (Jan 13, 2018)
17-50184186-G-C		Osteogenesis imperfecta • Ehlers-Danlos syndrome, arthrochalasia type • Infantile cortical hyperostosis	Uncertain significance (Mar 30, 2018)
17-50184237-G-A		Osteogenesis imperfecta • Ehlers-Danlos syndrome, arthrochalasia type • Infantile cortical hyperostosis	Benign/Likely benign (Jan 13, 2018)
17-50184269-C-T		Osteogenesis imperfecta • Ehlers-Danlos syndrome, arthrochalasia type • Infantile cortical hyperostosis	Benign/Likely benign (May 12, 2021)
17-50184297-G-C		Osteogenesis imperfecta • Ehlers-Danlos syndrome, arthrochalasia type • Infantile cortical hyperostosis	Uncertain significance (Jan 13, 2018)
17-50184327-A-C		Infantile cortical hyperostosis • Ehlers-Danlos syndrome, arthrochalasia type • Osteogenesis imperfecta	Benign (Jan 13, 2018)
17-50184337-G-C		Infantile cortical hyperostosis • Osteogenesis imperfecta • Ehlers-Danlos syndrome, arthrochalasia type	Conflicting classifications of pathogenicity (Apr 01, 2023)
17-50184351-G-A		Infantile cortical hyperostosis • Ehlers-Danlos syndrome, arthrochalasia type • Osteogenesis imperfecta	Uncertain significance (Jan 13, 2018)
17-50184414-C-T		Ehlers-Danlos syndrome, arthrochalasia type • Osteogenesis imperfecta • Infantile cortical hyperostosis	Benign/Likely benign (Oct 09, 2021)
17-50184415-G-A		Osteogenesis imperfecta • Infantile cortical hyperostosis • Ehlers-Danlos syndrome, arthrochalasia type	Uncertain significance (Jan 12, 2018)
17-50184451-GA-G			Likely benign (Oct 01, 2021)
17-50184456-AT-A		Osteogenesis Imperfecta, Dominant • Ehlers-Danlos syndrome type 7A • Infantile cortical hyperostosis	Uncertain significance (Jun 14, 2016)
17-50184470-ATC-A		Infantile cortical hyperostosis • Osteogenesis Imperfecta, Dominant • Ehlers-Danlos syndrome type 7A	Uncertain significance (Jun 14, 2016)
17-50184470-ATCC-A		Ehlers-Danlos syndrome type 7A • Infantile cortical hyperostosis • Osteogenesis Imperfecta, Dominant	Uncertain significance (Jun 14, 2016)
17-50184472-CCA-C		Infantile cortical hyperostosis • Ehlers-Danlos syndrome type 7A • Osteogenesis Imperfecta, Dominant	Uncertain significance (Jun 14, 2016)
17-50184473-CACA-C		Osteogenesis Imperfecta, Dominant • Infantile cortical hyperostosis • Ehlers-Danlos syndrome type 7A	Conflicting classifications of pathogenicity (May 20, 2021)
17-50184474-AC-A		Infantile cortical hyperostosis • Ehlers-Danlos syndrome type 7A • Osteogenesis Imperfecta, Dominant	Uncertain significance (Jun 14, 2016)
17-50184475-C-A		Osteogenesis imperfecta • Ehlers-Danlos syndrome, arthrochalasia type • Infantile cortical hyperostosis	Conflicting classifications of pathogenicity (May 11, 2021)
17-50184475-CA-C			Likely benign (May 10, 2021)
17-50184475-CAA-C			Benign (May 10, 2021)
17-50184475-C-CA			Benign (May 12, 2021)
17-50184491-A-G		Infantile cortical hyperostosis • Ehlers-Danlos syndrome, arthrochalasia type • Osteogenesis imperfecta	Conflicting classifications of pathogenicity (May 10, 2021)
17-50184493-AAG-A		Osteogenesis Imperfecta, Dominant • Infantile cortical hyperostosis • Ehlers-Danlos syndrome type 7A	Uncertain significance (Jun 14, 2016)
17-50184502-ATC-A		Infantile cortical hyperostosis • Ehlers-Danlos syndrome type 7A • Osteogenesis Imperfecta, Dominant	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL1A1	protein_coding	protein_coding	ENST00000225964	51	18344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.06e-11	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.53	600	898	0.668	0.0000568	9116
Missense in Polyphen		20	52.573	0.38042		494
Synonymous	-1.00	353	330	1.07	0.0000227	3284
Loss of Function	8.23	4	86.8	0.0461	0.00000512	938

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000304	0.0000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000282	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen).
• Disease: DISEASE: Caffey disease (CAFFD) [MIM:114000]: Characterized by an infantile episode of massive subperiosteal new bone formation that typically involves the diaphyses of the long bones, mandible, and clavicles. The involved bones may also appear inflamed, with painful swelling and systemic fever often accompanying the illness. The bone changes usually begin before 5 months of age and resolve before 2 years of age. {ECO:0000269|PubMed:15864348}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ehlers-Danlos syndrome, classic type, 1 (EDSCL1) [MIM:130000]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. The main features of classic Ehlers-Danlos syndrome are joint hypermobility and dislocation, and fragile, bruisable skin. EDSCL1 inheritance is autosomal dominant. {ECO:0000269|PubMed:10739762, ECO:0000269|PubMed:17211858}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; DISEASE: Ehlers-Danlos syndrome, arthrochalasia type, 1 (EDSARTH1) [MIM:130060]: A form of Ehlers-Danlos syndrome, a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDSARTH1 is an autosomal dominant form characterized by frequent congenital hip dislocation and extreme joint laxity with recurrent joint subluxations and minimal skin involvement. {ECO:0000269|PubMed:18409203, ECO:0000269|PubMed:9295084}. 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:1634225, ECO:0000269|PubMed:16638323, ECO:0000269|PubMed:16705691, ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:1718984, ECO:0000269|PubMed:1737847, ECO:0000269|PubMed:17875077, ECO:0000269|PubMed:18670065, ECO:0000269|PubMed:24682174, ECO:0000269|PubMed:2794057, ECO:0000269|PubMed:3244312, ECO:0000269|PubMed:8223589}. 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:1460047, ECO:0000269|PubMed:1511982, ECO:0000269|PubMed:1613761, ECO:0000269|PubMed:16566045, ECO:0000269|PubMed:16786509, ECO:0000269|PubMed:18670065, ECO:0000269|PubMed:1874719, ECO:0000269|PubMed:18996919, ECO:0000269|PubMed:1939261, ECO:0000269|PubMed:1953667, ECO:0000269|PubMed:2035536, ECO:0000269|PubMed:2036375, ECO:0000269|PubMed:2037280, ECO:0000269|PubMed:2116413, ECO:0000269|PubMed:2211725, ECO:0000269|PubMed:2339700, ECO:0000269|PubMed:2470760, ECO:0000269|PubMed:25958000, ECO:0000269|PubMed:2777764, ECO:0000269|PubMed:2794057, ECO:0000269|PubMed:2913053, ECO:0000269|PubMed:3016737, ECO:0000269|PubMed:3108247, ECO:0000269|PubMed:3403550, ECO:0000269|PubMed:3667599, ECO:0000269|PubMed:7520724, ECO:0000269|PubMed:7679635, ECO:0000269|PubMed:7691343, ECO:0000269|PubMed:7961597, ECO:0000269|PubMed:8100209, ECO:0000269|PubMed:8349697, ECO:0000269|PubMed:8349698, ECO:0000269|PubMed:8364588, ECO:0000269|PubMed:8456808, ECO:0000269|PubMed:8786074, ECO:0000269|PubMed:9143923, ECO:0000269|Ref.49, ECO:0000269|Ref.52}. 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:16879195, ECO:0000269|PubMed:1770532, ECO:0000269|PubMed:18670065, ECO:0000269|PubMed:2037280, ECO:0000269|PubMed:2511192, ECO:0000269|PubMed:2794057, ECO:0000269|PubMed:7691343, ECO:0000269|PubMed:7881420, ECO:0000269|PubMed:8019571, ECO:0000269|PubMed:8364588, ECO:0000269|PubMed:8456809, ECO:0000269|PubMed:8669434, ECO:0000269|PubMed:8723681, ECO:0000269|PubMed:9101304}. 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:16786509, ECO:0000269|PubMed:16879195, ECO:0000269|PubMed:1770532, ECO:0000269|PubMed:17875077, ECO:0000269|PubMed:1988452, ECO:0000269|PubMed:2745420, ECO:0000269|PubMed:7691343, ECO:0000269|PubMed:7982948, ECO:0000269|PubMed:8094076, ECO:0000269|PubMed:8339541, ECO:0000269|PubMed:9600458}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Osteoporosis (OSTEOP) [MIM:166710]: A systemic skeletal disorder characterized by decreased bone mass and deterioration of bone microarchitecture without alteration in the composition of bone. The result is fragile bones and an increased risk of fractures, even after minimal trauma. Osteoporosis is a chronic condition of multifactorial etiology and is usually clinically silent until a fracture occurs. {ECO:0000269|PubMed:8841196, ECO:0000269|PubMed:9535665}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving COL1A1 is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGF.
• 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;Aminocaproic Acid Action Pathway;Tranexamic Acid Action Pathway;Urokinase Action Pathway;Reteplase Action Pathway;Streptokinase Action Pathway;Tenecteplase Action Pathway;Alteplase Action Pathway;Anistreplase Action Pathway;Aprotinin Action Pathway;Phenindione Action Pathway;Dicoumarol Action Pathway;Warfarin Action Pathway;Acenocoumarol Action Pathway;Coagulation ;Bivalirudin Action Pathway;Argatroban Action Pathway;Ardeparin Action Pathway;Heparin Action Pathway;Fondaparinux Action Pathway;Enoxaparin Action Pathway;Phenprocoumon Action Pathway;Dicumarol Action Pathway;Ximelagatran Action Pathway;Lepirudin Action Pathway;miR-targeted genes in epithelium - TarBase;miR-targeted genes in muscle cell - TarBase;Focal Adhesion;Osteoblast Signaling;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;miR-509-3p alteration of YAP1-ECM axis;Protein alkylation leading to liver fibrosis;PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;Senescence and Autophagy in Cancer;RUNX2 regulates osteoblast differentiation;RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Gene expression (Transcription);Vesicle-mediated transport;Generic Transcription Pathway;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;RNA Polymerase II Transcription;Collagen formation;Extracellular matrix organization;Beta3 integrin cell surface interactions;Integrin;VEGFR3 signaling in lymphatic endothelium;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors;Beta1 integrin cell surface interactions;Syndecan-1-mediated signaling events;IL4-mediated signaling events;Integrins in angiogenesis (Consensus)

Recessive Scores

• pRec: 0.991

Intolerance Scores

• loftool: 0.00406
• rvis_EVS: -1.79
• rvis_percentile_EVS: 2.26

Haploinsufficiency Scores

• pHI: 0.992
• hipred: Y
• hipred_score: 0.774
• ghis: 0.670

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Col1a1
• Phenotype: 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; craniofacial phenotype; vision/eye 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); hematopoietic system phenotype; 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); reproductive system phenotype; pigmentation phenotype; neoplasm; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton 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

Zebrafish Information Network

• Gene name: col1a1a
• Affected structure: osteoblast
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: skeletal system development;ossification;blood vessel development;osteoblast differentiation;intramembranous ossification;endochondral ossification;blood coagulation;visual perception;sensory perception of sound;response to mechanical stimulus;positive regulation of epithelial to mesenchymal transition;negative regulation of cell-substrate adhesion;protein transport;platelet activation;extracellular matrix organization;collagen fibril organization;positive regulation of cell migration;response to corticosteroid;response to estradiol;collagen biosynthetic process;protein localization to nucleus;tooth mineralization;collagen-activated tyrosine kinase receptor signaling pathway;response to hydrogen peroxide;response to peptide hormone;skin development;skin morphogenesis;cellular response to fibroblast growth factor stimulus;tooth eruption;positive regulation of transcription, DNA-templated;embryonic skeletal system development;regulation of immune response;leukocyte migration;response to cAMP;response to hyperoxia;face morphogenesis;bone trabecula formation;cartilage development involved in endochondral bone morphogenesis;protein heterotrimerization;cellular response to amino acid stimulus;cellular response to mechanical stimulus;cellular response to retinoic acid;cellular response to vitamin E;cellular response to tumor necrosis factor;cellular response to epidermal growth factor stimulus;cellular response to transforming growth factor beta stimulus;positive regulation of canonical Wnt signaling pathway;cellular response to fluoride
• Cellular component: extracellular region;collagen type I trimer;extracellular space;cytoplasm;endoplasmic reticulum lumen;Golgi apparatus;secretory granule;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: protease binding;extracellular matrix structural constituent;protein binding;extracellular matrix structural constituent conferring tensile strength;identical protein binding;metal ion binding;platelet-derived growth factor binding