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COL27A1 Gene(Protein Coding)

Collagen Type XXVII Alpha 1 Chain

GCID:
GC09P114269
GIFtS:
47
Genes Participants
UDN Logo

Aliases for COL27A1 Gene

Aliases for COL27A1 Gene

  • Collagen Type XXVII Alpha 1 Chain 2 3 5
  • Collagen, Type XXVII, Alpha 1 2 3
  • Collagen Alpha-1(XXVII) Chain 3
  • Collagen Type XXVII Alpha 1 2
  • KIAA1870 4
  • STLS 3

External Ids for COL27A1 Gene

Previous GeneCards Identifiers for COL27A1 Gene

  • GC09P110371
  • GC09P112294
  • GC09P112293
  • GC09P113997
  • GC09P115957
  • GC09P116917
  • GC09P086524
  • GC09P114155
  • GC09P114156
  • GC09P114268
  • GC09P114266
  • GC09P114267

Summaries for COL27A1 Gene

Entrez Gene Summary for COL27A1 Gene

  • This gene encodes a member of the fibrillar collagen family, and plays a role during the calcification of cartilage and the transition of cartilage to bone. The encoded protein product is a preproprotein. It includes an N-terminal signal peptide, which is followed by an N-terminal propetide, mature peptide and a C-terminal propeptide. The N-terminal propeptide contains thrombospondin N-terminal-like and laminin G-like domains. The mature peptide is a major triple-helical region. The C-terminal propeptide, also known as COLFI domain, plays crucial roles in tissue growth and repair. Mutations in this gene cause Steel syndrome. Alternatively spliced transcript variants have been found, but the full-length nature of some variants has not been determined. [provided by RefSeq, Sep 2014]

GeneCards Summary for COL27A1 Gene

COL27A1 (Collagen Type XXVII Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL27A1 include Steel Syndrome and Cervix Uteri Carcinoma In Situ. Among its related pathways are ERK Signaling and Collagen chain trimerization. Gene Ontology (GO) annotations related to this gene include extracellular matrix structural constituent. An important paralog of this gene is COL24A1.

UniProtKB/Swiss-Prot for COL27A1 Gene

  • Plays a role during the calcification of cartilage and the transition of cartilage to bone.

Gene Wiki entry for COL27A1 Gene

Additional gene information for COL27A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL27A1 Gene

Genomics for COL27A1 Gene

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  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for COL27A1 Gene

Promoters and enhancers for COL27A1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH09J114154 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 658.9 +27.1 27148 5.4 ARID4B SIN3A ZNF48 YY1 GLIS2 ZNF143 FOS KLF13 RXRA MXD4 COL27A1 CDC26 LOC105376225 GC09P114793
GH09J114168 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.3 +38.2 38233 0.1 COL27A1 MIR455 GC09P114793 LOC105376225
GH09J114169 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 35 +43.4 43429 9.5 PKNOX1 MLX ARID4B DMAP1 ZNF48 ETS1 YY1 FOS RXRA SP5 COL27A1 PRPF4 MIR455 ORM1 GC09P114793 GC09P114319 GC09P114318
GH09J114180 Enhancer 0.9 Ensembl ENCODE dbSUPER 29.7 +51.1 51051 2.4 SP1 RXRA ZNF189 HNF4G HNF4A NR2F2 COL27A1 MIR455 GC09P114793 GC09P114318 GC09P114319
GH09J113150 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.6 -976.8 -976847 6.2 PKNOX1 ATF1 ZFP64 ARID4B SIN3A BRCA1 ZNF48 ETS1 ZNF121 GLIS2 SLC31A2 PIR43385 PRPF4 ZNF618 COL27A1 FKBP15 BSPRY LOC105376223 WDR31 SNX30
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL27A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL27A1 gene promoter:
  • PPAR-alpha
  • Nkx2-5
  • Hlf
  • ISGF-3
  • RelA
  • NCX
  • Egr-4
  • Nkx5-1
  • XBP-1
  • RFX1

Genomic Locations for COL27A1 Gene

Genomic Locations for COL27A1 Gene
chr9:114,130,331-114,312,516
(GRCh38/hg38)
Size:
182,186 bases
Orientation:
Plus strand
chr9:116,917,840-117,074,791
(GRCh37/hg19)
Size:
156,952 bases
Orientation:
Plus strand

Genomic View for COL27A1 Gene

Genes around COL27A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL27A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL27A1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for COL27A1 Gene

Proteins for COL27A1 Gene

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  1. Antibody
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  • Protein details for COL27A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IZC6-CORA1_HUMAN
    Recommended name:
    Collagen alpha-1(XXVII) chain
    Protein Accession:
    Q8IZC6
    Secondary Accessions:
    • Q66K43
    • Q96JF7

    Protein attributes for COL27A1 Gene

    Size:
    1860 amino acids
    Molecular mass:
    186892 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB47499.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for COL27A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL27A1 Gene

Protein Expression for COL27A1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for COL27A1 Gene

  • Glycosylation at posLast=17691769 and Asn271
  • Modification sites at PhosphoSitePlus

Other Protein References for COL27A1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for COL27A1 Gene

Domains & Families for COL27A1 Gene

Gene Families for COL27A1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for COL27A1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for COL27A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8IZC6

UniProtKB/Swiss-Prot:

CORA1_HUMAN :
  • The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
  • Belongs to the fibrillar collagen family.
Domain:
  • The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
Family:
  • Belongs to the fibrillar collagen family.
genes like me logo Genes that share domains with COL27A1: view

Function for COL27A1 Gene

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  2. CRISPR
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Molecular function for COL27A1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role during the calcification of cartilage and the transition of cartilage to bone.

Phenotypes From GWAS Catalog for COL27A1 Gene

Gene Ontology (GO) - Molecular Function for COL27A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with COL27A1: view
genes like me logo Genes that share phenotypes with COL27A1: view

Human Phenotype Ontology for COL27A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for COL27A1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL27A1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for COL27A1 Gene

Localization for COL27A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL27A1 Gene

Secreted, extracellular space, extracellular matrix. Note=Found on some small banded collagen fibrils and meshworks. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL27A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for COL27A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005583 fibrillar collagen trimer IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL27A1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for COL27A1 Gene

Pathways & Interactions for COL27A1 Gene

genes like me logo Genes that share pathways with COL27A1: view

Interacting Proteins for COL27A1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000348385%0d%0a9606.ENSP00000297848%0d%0a9606.ENSP00000369889%0d%0a9606.ENSP00000316030%0d%0a9606.ENSP00000351767%0d%0a9606.ENSP00000303153%0d%0a
Selected Interacting proteins: ENSP00000348385 for COL27A1 Gene via STRING

GPS-Prot Interaction Network for COL27A1

Gene Ontology (GO) - Biological Process for COL27A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003431 growth plate cartilage chondrocyte development IEA --
GO:0030198 extracellular matrix organization IEA --
genes like me logo Genes that share ontologies with COL27A1: view

No data available for SIGNOR curated interactions for COL27A1 Gene

Drugs & Compounds for COL27A1 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for COL27A1 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for COL27A1 Gene

(11) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(231) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL27A1 Gene

Collagen, type XXVII, alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL27A1

Alternative Splicing Database (ASD) splice patterns (SP) for COL27A1 Gene

No ASD Table

Relevant External Links for COL27A1 Gene

GeneLoc Exon Structure for
COL27A1
ECgene alternative splicing isoforms for
COL27A1

Expression for COL27A1 Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL27A1 Gene

mRNA expression in normal human tissues for COL27A1 Gene
mRNA expression by GTEx for COL27A1 GenemRNA expression by BioGPS for COL27A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL27A1 Gene

This gene is overexpressed in Brain - Cerebellum (x5.8), Brain - Cerebellar Hemisphere (x5.4), and Cervix - Ectocervix (x4.5).

Protein differential expression in normal tissues from HIPED for COL27A1 Gene

This gene is overexpressed in Breast (37.2) and Bone (18.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for COL27A1 Gene



Protein tissue co-expression partners for COL27A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL27A1 Gene:

COL27A1

SOURCE GeneReport for Unigene cluster for COL27A1 Gene:

Hs.494892

Evidence on tissue expression from TISSUES for COL27A1 Gene

  • Skin(4.2)
  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL27A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • respiratory
  • skeleton
Regions:
Head and neck:
  • eye
  • face
  • forehead
  • head
  • nose
  • skull
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
Limb:
  • arm
  • forearm
  • radius
  • upper limb
General:
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with COL27A1: view

No data available for mRNA Expression by UniProt/SwissProt for COL27A1 Gene

Orthologs for COL27A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL27A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia COL27A1 34 33
  • 96.64 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia COL27A1 34 33
  • 88.3 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia COL27A1 34 33
  • 87.19 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Col27a1 16 34 33
  • 82.3 (n)
rat
(Rattus norvegicus)
 Mammalia Col27a1 33
  • 81.91 (n)
oppossum
(Monodelphis domestica)
 Mammalia COL27A1 34
  • 68 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 34 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves COL27A1 33
  • 68.96 (n)
lizard
(Anolis carolinensis)
 Reptilia COL27A1 34
  • 61 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC100490770 33
  • 63.16 (n)
zebrafish
(Danio rerio)
 Actinopterygii col27a1b 34
  • 58 (a)
 OneToMany
col27a1a 34
  • 55 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 38 (a)
 OneToMany
Species where no ortholog for COL27A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for COL27A1 Gene

ENSEMBL:
Gene Tree for COL27A1 (if available)
TreeFam:
Gene Tree for COL27A1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COL27A1: view image

Paralogs for COL27A1 Gene

Paralogs for COL27A1 Gene

(5) SIMAP similar genes for COL27A1 Gene using alignment to 4 proteins:

  • CORA1_HUMAN
  • H0YD40_HUMAN
  • Q5T1U7_HUMAN
  • Q9HAA3_HUMAN
genes like me logo Genes that share paralogs with COL27A1: view

Variants for COL27A1 Gene

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Sequence variations from dbSNP and Humsavar for COL27A1 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs140950220 pathogenic, Steel syndrome, not provided, Steel syndrome (STLS) [MIM:615155] 114,195,977(+) G/C 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000004375 -- 114,204,751(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000021744 -- 114,171,030(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000039044 -- 114,234,937(+) G/A intron_variant
rs1000050541 -- 114,245,380(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for COL27A1 Gene

Variant ID Type Subtype PubMed ID
dgv12856n54 CNV loss 21841781
dgv12857n54 CNV loss 21841781
dgv12858n54 CNV loss 21841781
dgv12859n54 CNV gain 21841781
dgv12860n54 CNV gain 21841781
dgv33e196 CNV duplication 17116639
dgv7706n100 CNV gain 25217958
dgv946n27 CNV loss 19166990
dgv947n27 CNV loss 19166990
dgv948n27 CNV gain 19166990
dgv949n27 CNV gain 19166990
esv2761285 CNV gain 21179565
esv2761551 CNV loss 21179565
esv3302446 CNV tandem duplication 20981092
esv3385334 CNV duplication 20981092
esv3621549 CNV gain 21293372
esv3621553 CNV loss 21293372
nsv1116481 OTHER inversion 24896259
nsv1124466 CNV deletion 24896259
nsv466536 CNV loss 19166990
nsv466547 CNV gain 19166990
nsv471320 CNV gain 18288195
nsv474605 CNV novel sequence insertion 20440878
nsv509319 CNV insertion 20534489
nsv522296 CNV loss 19592680
nsv528823 CNV gain 19592680
nsv615232 CNV loss 21841781
nsv615233 CNV gain 21841781
nsv615239 CNV loss 21841781
nsv615240 CNV gain 21841781
nsv615244 CNV gain 21841781
nsv6677 CNV insertion 18451855

Variation tolerance for COL27A1 Gene

Residual Variation Intolerance Score: 92.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 20.51; 99.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL27A1 Gene

Human Gene Mutation Database (HGMD)
COL27A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL27A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL27A1 Gene

Disorders for COL27A1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for COL27A1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
steel syndrome
  • stls
cervix uteri carcinoma in situ
  • carcinoma in situ of cervix
hypertelorism
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CORA1_HUMAN
  • Steel syndrome (STLS) [MIM:615155]: A syndrome characterized by dislocated hips and radial heads, fusion of carpal bones, short stature, scoliosis, and cervical spine anomalies. Facial features include prominent forehead, long oval-shaped face, hypertelorism and broad nasal bridge. {ECO:0000269 PubMed:24986830}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for COL27A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with COL27A1: view

No data available for Genatlas for COL27A1 Gene

Publications for COL27A1 Gene

  1. Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1. (PMID: 12714037) Pace JM … Byers PH (Matrix biology : journal of the International Society for Matrix Biology 2003) 2 3 4 58
  2. Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population. (PMID: 24986830) Gonzaga-Jauregui C … Hecht JT (European journal of human genetics : EJHG 2015) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 44 58
  5. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira AR … Marazita ML (Genetics in medicine : official journal of the American College of Medical Genetics 2008) 3 44 58

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