Reviewed, UniProtKB/Swiss-Prot Q03692 (COAA1_HUMAN)

Names and origin

Protein names

Recommended name:
    Collagen alpha-1(X) chain

Gene names

Name:

COL10A1

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	680 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Type X collagen is a product of hyperthrophic chondrotocytes and has been localized to presumptive mineralization zones of hyaline cartilage.
Subunit structure	Homotrimer.
Subcellular location	Secreted › extracellular space › extracellular matrix By similarity.
Post-translational modification	Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
Involvement in disease	Defects in COL10A1 are the cause of Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500]. SMCD is a dominantly inherited disorder of the osseous skeleton. The cardinal features of the phenotype are mild short stature, coxa vara and a waddling gait. Radiography usually shows sclerosis of the ribs, flaring of the metaphyses, and a wide irregular growth plate, especially of the knees. A variant form of SMCD is spondylometaphyseal dysplasia Japanese type. It is characterized by spinal involvement comprising mild platyspondyly, vertebral body abnormalities, and end-plate irregularity. Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.17 Ref.18
Sequence similarities	Contains 1 C1q domain.

Ontologies

Keywords
Cellular component	Extracellular matrix Secreted
Coding sequence diversity	Polymorphism
Disease	Disease mutation
Domain	Collagen Repeat Signal
Ligand	Calcium Metal-binding
PTM	Hydroxylation
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	skeletal system development Traceable author statement. Source: ProtInc
Cellular component	collagen Traceable author statement. Source: ProtInc extracellular space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 18

18

Potential

Chain

19 – 680

662

Collagen alpha-1(X) chain

PRO_0000005770

Regions

Domain

547 – 680

134

C1q

Region

19 – 56

38

Nonhelical region (NC2)

Region

57 – 519

463

Triple-helical region

Region

520 – 680

161

Nonhelical region (NC1)

Sites

Metal binding

634

1

Calcium

Natural variations

Natural variant

18

1

G → E in SMCD. Ref.15 Ref.18

VAR_001838

Natural variant

18

1

G → R in SMCD. Ref.15 Ref.18

VAR_001839

Natural variant

27

1

M → T: dbSNP rs1064583. Ref.18 Ref.1

VAR_023186

Natural variant

98

1

G → R: dbSNP rs2243370.

VAR_048767

Natural variant

198

1

R → H Ref.18

VAR_023187

Natural variant

545

1

G → R: dbSNP rs2228547. Ref.13 Ref.18

VAR_001840

Natural variant

582

1

Y → D in SMCD. Ref.18

VAR_023188

Natural variant

591

1

C → R in SMCD. Ref.11 Ref.18

VAR_001841

Natural variant

595

1

G → E in SMCD and spondylometaphyseal dysplasia Japanese type.

VAR_001842

Natural variant

595

1

G → R in SMCD. Ref.13 Ref.18

VAR_023189

Natural variant

597

1

Y → C in SMCD. Ref.13 Ref.17 Ref.18

VAR_008039

Natural variant

597

1

Y → H in SMCD. Ref.13 Ref.17 Ref.18

VAR_001843

Natural variant

598

1

Y → D in SMCD. Ref.10 Ref.18

VAR_001844

Natural variant

600

1

S → P in SMCD. Ref.14 Ref.18

VAR_001845

Natural variant

603

1

V → M Ref.18

VAR_023190

Natural variant

614

1

L → P in SMCD. Ref.10 Ref.18

VAR_001846

Natural variant

617

1

N → K in SMCD. Ref.13 Ref.18

VAR_001847

Natural variant

618

1

G → V in SMCD. Ref.12 Ref.18

VAR_001848

Natural variant

644

1

L → R in SMCD. Ref.13 Ref.18

VAR_001849

Natural variant

648

1

D → G in SMCD. Ref.13 Ref.18

VAR_001850

Natural variant

651

1

W → R in SMCD. Ref.18

VAR_023191

Natural variant

653

1

Q → P in SMCD. Ref.18

VAR_023192

Natural variant

671

1

S → P in SMCD. Ref.18

VAR_023193

Experimental info

Sequence conflict

500

1

H → P Ref.1

Sequence conflict

500

1

H → P Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

680

Helix Strand Turn

Details...

Beta strand

553 – 557

5

Beta strand

560 – 562

3

Beta strand

573 – 576

4

Turn

584 – 586

3

Beta strand

595 – 616

22

Beta strand

619 – 626

8

Beta strand

634 – 644

11

Beta strand

649 – 653

5

Beta strand

659 – 663

5

Beta strand

666 – 668

3

Beta strand

671 – 679

9

Sequences

	Sequence		Length	Mass (Da)
	Q03692-1 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: E2F98E53E7882459	FASTA	680	66,158
	10 20 30 40 50 60 MLPQIPFLLL VSLNLVHGVF YAERYQMPTG IKGPLPNTKT QFFIPYTIKS KGIAVRGEQG 70 80 90 100 110 120 TPGPPGPAGP RGHPGPSGPP GKPGYGSPGL QGEPGLPGPP GPSAVGKPGV PGLPGKPGER 130 140 150 160 170 180 GPYGPKGDVG PAGLPGPRGP PGPPGIPGPA GISVPGKPGQ QGPTGAPGPR GFPGEKGAPG 190 200 210 220 230 240 VPGMNGQKGE MGYGAPGRPG ERGLPGPQGP TGPSGPPGVG KRGENGVPGQ PGIKGDRGFP 250 260 270 280 290 300 GEMGPIGPPG PQGPPGERGP EGIGKPGAAG APGQPGIPGT KGLPGAPGIA GPPGPPGFGK 310 320 330 340 350 360 PGLPGLKGER GPAGLPGGPG AKGEQGPAGL PGKPGLTGPP GNMGPQGPKG IPGSHGLPGP 370 380 390 400 410 420 KGETGPAGPA GYPGAKGERG SPGSDGKPGY PGKPGLDGPK GNPGLPGPKG DPGVGGPPGL 430 440 450 460 470 480 PGPVGPAGAK GMPGHNGEAG PRGAPGIPGT RGPIGPPGIP GFPGSKGDPG SPGPPGPAGI 490 500 510 520 530 540 ATKGLNGPTG PPGPPGPRGH SGEPGLPGPP GPPGPPGQAV MPEGFIKAGQ RPSLSGTPLV 550 560 570 580 590 600 SANQGVTGMP VSAFTVILSK AYPAIGTPIP FDKILYNRQQ HYDPRTGIFT CQIPGIYYFS 610 620 630 640 650 660 YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN 670 680 GLYSSEYVHS SFSGFLVAPM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The human collagen X gene. Complete primary translated sequence and chromosomal localization." Thomas J.T., Cresswell C.J., Rash B., Nicolai H., Jones T., Solomon E., Grant M.E., Boot-Handford R.P. Biochem. J. 280:617-623(1991) [PubMed: 1764025] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT THR-27.
[2]	"Genomic organization and full-length cDNA sequence of human collagen X." Reichenberger E., Beier F., LuValle P., Olsen B.R., von der Mark K., Bertling W.M. FEBS Lett. 311:305-310(1992) [PubMed: 1397333] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	Beier F., Lammi M.B., von der Mark K. Submitted (JUN-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"The DNA sequence and analysis of human chromosome 6." Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S. Nature 425:805-811(2003) [PubMed: 14574404] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"Cloning of the human and mouse type X collagen genes and mapping of the mouse type X collagen gene to chromosome 10." Apte S.S., Seldin M.F., Hayashi M., Olsen B.R. Eur. J. Biochem. 206:217-224(1992) [PubMed: 1587271] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 52-680.
[6]	"Cloning of human alpha 1(X) collagen DNA and localization of the COL10A1 gene to the q21-q22 region of human chromosome 6." Apte S., Mattei M.-G., Olsen B.R. FEBS Lett. 282:393-396(1991) [PubMed: 2037056] [Abstract] Cited for: NUCLEOTIDE SEQUENCE OF 561-666.
[7]	"In situ hybridization studies on the expression of type X collagen in fetal human cartilage." Reichenberger E., Aigner T., von der Mark K., Stoeb H., Bertling W. Dev. Biol. 148:562-572(1991) [PubMed: 1743401] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 547-655.
[8]	"Insight into Schmid metaphyseal chondrodysplasia from the crystal structure of the collagen X NC1 domain trimer." Bogin O., Kvansakul M., Rom E., Singer J., Yayon A., Hohenester E. Structure 10:165-173(2002) [PubMed: 11839302] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 521-680, CALCIUM-BINDING.
[9]	"Mutations in fibrillar collagens (types I, II, III, and XI), fibril-associated collagen (type IX), and network-forming collagen (type X) cause a spectrum of diseases of bone, cartilage, and blood vessels." Kuivaniemi H., Tromp G., Prockop D.J. Hum. Mutat. 9:300-315(1997) [PubMed: 9101290] [Abstract] Cited for: REVIEW ON VARIANTS.
[10]	"Amino acid substitutions of conserved residues in the carboxyl-terminal domain of the alpha 1(X) chain of type X collagen occur in two unrelated families with metaphyseal chondrodysplasia type Schmid." Wallis G.A., Rash B., Sweetman W.A., Thomas J.T., Super M., Evans G., Grant M.E., Boot-Handford R.P. Am. J. Hum. Genet. 54:169-178(1994) [PubMed: 8304336] [Abstract] Cited for: VARIANTS SMCD ASP-598 AND PRO-614.
[11]	"Additional mutations of type X collagen confirm COL10A1 as the Schmid metaphyseal chondrodysplasia locus." McIntosh I., Abbott M.H., Warman M.L., Olsen B.R., Francomano C.A. Hum. Mol. Genet. 3:303-307(1994) [PubMed: 8004099] [Abstract] Cited for: VARIANT SMCD ARG-591.
[12]	"Type X collagen multimer assembly in vitro is prevented by a Gly618 to Val mutation in the alpha 1(X) NC1 domain resulting in Schmid metaphyseal chondrodysplasia." Chan D., Cole W.G., Rogers J.G., Bateman J.F. J. Biol. Chem. 270:4558-4562(1995) [PubMed: 7876225] [Abstract] Cited for: VARIANT SMCD VAL-618.
[13]	"Mutations in three subdomains of the carboxy-terminal region of collagen type X account for most of the Schmid metaphyseal dysplasias." Bonaventure J., Chaminade F., Maroteaux P. Hum. Genet. 96:58-64(1995) [PubMed: 7607655] [Abstract] Cited for: VARIANTS SMCD ARG-545; GLU-595; HIS-597; LYS-617; ARG-644 AND GLY-648.
[14]	"Mutations within the gene encoding the alpha 1 (X) chain of type X collagen (COL10A1) cause metaphyseal chondrodysplasia type Schmid but not several other forms of metaphyseal chondrodysplasia." Wallis G.A., Rash B., Sykes B., Bonaventure J., Maroteaux P., Zabel B., Wynne-Davies R., Grant M.E., Boot-Handford R.P. J. Med. Genet. 33:450-457(1996) [PubMed: 8782043] [Abstract] Cited for: VARIANT SMCD PRO-600.
[15]	"Mutations in the N-terminal globular domain of the type X collagen gene (COL10A1) in patients with schmid metaphyseal chondrodysplasia." Ikegawa S., Nakamura K., Nagano A., Haga N., Nakamura Y. Hum. Mutat. 9:131-135(1997) [PubMed: 9067753] [Abstract] Cited for: VARIANTS SMCD GLU-18 AND ARG-18.
[16]	"Mutation of the type X collagen gene 'COL10A1' causes spondylometaphyseal dysplasia." Ikegawa S., Nishimura G., Nagai T., Hasegawa T., Ohashi H., Nakamura Y. Am. J. Hum. Genet. 63:1659-1662(1998) [PubMed: 9837818] [Abstract] Cited for: VARIANT SPONDYLOMETAPHYSEAL DYSPLASIA JAPANESE TYPE GLU-595.
[17]	"Novel missense mutation resulting in the substitution of tyrosine by cysteine at codon 597 of the type X collagen gene associated with Schmid metaphyseal chondrodysplasia." Sawai H., Ida A., Nakata Y., Koyama K. J. Hum. Genet. 43:259-261(1998) [PubMed: 9852679] [Abstract] Cited for: VARIANT SMCD CYS-597.
[18]	"Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia." Bateman J.F., Wilson R., Freddi S., Lamande S.R., Savarirayan R. Hum. Mutat. 25:525-534(2005) [PubMed: 15880705] [Abstract] Cited for: VARIANTS SMCD ARG-18; GLU-18; ASP-582; ARG-591; ARG-595; GLU-595; HIS-597; CYS-597; ASP-598; PRO-600; PRO-614; LYS-617; VAL-618; ARG-644; GLY-648; ARG-651; PRO-653 AND PRO-671, VARIANTS THR-27; HIS-198; ARG-545 AND MET-603.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases

EMBLGenBankDDBJ

X60382 Genomic DNA. Translation: CAA42933.1.
X65120 Genomic DNA. Translation: CAA46236.1.
X98568 Genomic DNA. Translation: CAA67178.1.
AL121963 Genomic DNA. Translation: CAB87590.1.
S68531 mRNA. Translation: AAC60615.1.
X58879 Genomic DNA. Translation: CAA41686.1.
M74050 Genomic DNA. Translation: AAA61221.1.
X72579, X72580 Genomic DNA. Translation: CAA51170.1.

IPI

IPI00011685.

PIR

CGHU1D. S26396.

RefSeq

NP_000484.2.

UniGene

Hs.520339

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GR3	X-ray	2.00	A	521-680	[»]

ModBase

Search...

Proteomic databases

PRIDE

Q03692.

Genome annotation databases

Ensembl

ENSG00000123500. Homo sapiens. [Contig view]

GeneID

1300.

KEGG

hsa:1300.

UCSC

uc003pwm.1. human.

Organism-specific databases

GeneCards

GC06M116546.

H-InvDB

HIX0032970.

HGNC

HGNC:2185. COL10A1.

MIM

120110. gene.
156500. phenotype.
184250. phenotype.

Orphanet

174. Metaphyseal chondrodysplasia, Schmid type.

PharmGKB

PA26701.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q03692.

HOVERGEN

Q03692.

OMA

Q03692. CRIPGIY.

Gene expression databases

ArrayExpress

Q03692.

Bgee

Q03692.

CleanEx

HS_COL10A1.

GermOnline

ENSG00000123500. Homo sapiens.

Family and domain databases

InterPro

IPR001073. C1q.
IPR008160. Collagen.
IPR008983. Tumour_necrosis_fac-like.
[Graphical view]

Gene3D

G3DSA:2.60.120.40. Tumour_necrosis_fac-like. 1 hit.

Pfam

PF00386. C1q. 1 hit.
PF01391. Collagen. 8 hits.
[Graphical view]

PRINTS

PR00007. COMPLEMNTC1Q.

ProDom

PD000007. Clg_helix. 2 hits.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00110. C1Q. 1 hit.
[Graphical view]

PROSITE

PS50871. C1Q. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

5279.

SOURCE

Search...

Entry information

Entry name

COAA1_HUMAN

Accession

Primary (citable) accession number: Q03692

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1997
Last modified:	July 7, 2009
This is version 97 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)