KERA (keratocan)

Gene

• Entrez ID: 11081
• Gene name: Keratocan
• Gene symbol: KERA
• Synonyms (NCBI Gene): CNA2, KTN, SLRR2B
• Chromosome: 12
• Chromosome location: 12q21.33
• Summary: The protein encoded by this gene is a keratan sulfate proteoglycan that is involved in corneal transparency. Defects in this gene are a cause of autosomal recessive cornea plana 2 (CNA2).[provided by RefSeq, May 2010]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121917858	T>C	Pathogenic	Coding sequence variant, missense variant
rs121917860	G>A,C	Pathogenic	Coding sequence variant, stop gained, missense variant
rs121917862	G>T	Pathogenic	Coding sequence variant, missense variant
rs121917863	G>A,C,T	Pathogenic	Coding sequence variant, stop gained, synonymous variant, missense variant
rs386833984	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs386833985	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs386833986	G>A	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs757611751	A>C	Pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018215	hsa-miR-335-5p	Microarray	18185580
MIRT1085147	hsa-miR-127-5p	CLIP-seq
MIRT1085148	hsa-miR-2116	CLIP-seq
MIRT1085149	hsa-miR-4639-5p	CLIP-seq
MIRT1085150	hsa-miR-4677-5p	CLIP-seq
MIRT1085151	hsa-miR-4719	CLIP-seq
MIRT1085152	hsa-miR-4735-5p	CLIP-seq
MIRT2253212	hsa-miR-2276	CLIP-seq
MIRT2253213	hsa-miR-3908	CLIP-seq
MIRT2253214	hsa-miR-3942-5p	CLIP-seq
MIRT2253215	hsa-miR-4703-5p	CLIP-seq
MIRT2253216	hsa-miR-4766-3p	CLIP-seq
MIRT2253217	hsa-miR-4772-3p	CLIP-seq
MIRT2452363	hsa-miR-155	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0005796	Component	Golgi lumen	TAS
GO:0007601	Process	Visual perception	IEA
GO:0031012	Component	Extracellular matrix	NAS	10802664
GO:0043202	Component	Lysosomal lumen	IEA
GO:0043202	Component	Lysosomal lumen	TAS
GO:0061303	Process	Cornea development in camera-type eye	IEA

Other IDs

• MIM: 603288
• HGNC: 6309
• e!Ensembl: ENSG00000139330

Protein

• UniProt ID: O60938
• Protein name: Keratocan (KTN) (Keratan sulfate proteoglycan keratocan)
• Protein function: May be important in developing and maintaining corneal transparency and for the structure of the stromal matrix.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13855	LRR_8	71 → 133	Leucine rich repeat	Repeat
  PF13855	LRR_8	142 → 204	Leucine rich repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Cornea (at protein level) (PubMed:10802664, PubMed:11683372). Increased expression in the stroma of keratoconus corneas (PubMed:11683372). Also detected in trachea, and in low levels, in intestine, skeletal muscle, ovary, lung and puta
• Sequence:

  MAGTICFIMWVLFITDTVWSRSVRQVYEVHDSDDWTIHDFECPMECFCPPSFPTALYCEN
  RGLKEIPAIPSRIWYLYLQNNLIETIPEKPFENATQLRWINLNKNKITNYGIEKGALSQL
  KKLLFLFLEDNELEEVPSPLPRSLEQLQLARNKVSRIPQGTFSNLENLTLLDLQNNKLVD
  NAFQRDTFKGLKNLMQLNMAKNALRNMPPRLPANTMQLFLDNNSIEGIPENYFNVIPKVA
  FLRLNHNKLSDEGLPSRGFDVSSILDLQLSHNQLTKVPRISAHLQHLHLDHNKIKSVNVS
  VICPSPSMLPAERDSFSYGPHLRYLRLDGNEIKPPIPMALMTCFRLLQAVII

• Sequence length: 352

Pathways

Reactome:

Keratan sulfate biosynthesis
Keratan sulfate degradation
Defective CHST6 causes MCDC1
Defective ST3GAL3 causes MCT12 and EIEE15
Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cornea plana 2	Pathogenic; Likely pathogenic	rs121917858, rs121917860, rs121917862, rs121917863, rs757611751, rs386833985, rs386833986	RCV000006892 RCV000006893 RCV000006894 RCV000006895 RCV000210915 RCV000049962 RCV000049963	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
KERA-related disorder	Pathogenic	rs758552587	RCV004758942	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL CORNEA PLANA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL MALFORMATION OF CORNEA NOS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEA PLANA	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEA PLANA 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEA PLANA 2, AUTOSOMAL RECESSIVE	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEAL DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIABETIC NEPHROPATHY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY CORNEAL DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IRIDO-CORNEO-TRABECULAR DYSGENESIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	BEFREE	30404605		★☆☆☆☆ Found in Text Mining only
Angle Closure Glaucoma	Angle Closure Glaucoma	BEFREE	25967529		★☆☆☆☆ Found in Text Mining only
Arcus Senilis	Arcus Senilis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	24879339		★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	24879339		★☆☆☆☆ Found in Text Mining only
Connective Tissue Diseases	Connective Tissue Disease	BEFREE	29760442		★☆☆☆☆ Found in Text Mining only
Cornea plana	Cornea Plana	BEFREE	11726611, 12975606, 15370545, 17558846, 17679937, 25967529, 28677912, 31059048, 7601455, 8723718, 8825624, 8929947		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cornea plana	Cornea Plana	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cornea Plana 1	Cornea plana	Pubtator	26099342, 28677912, 31059048	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEA PLANA 2	Cornea Plana	BEFREE	10802664, 11726611, 17558846, 17679937, 25967529		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CORNEA PLANA 2	Cornea Plana	UNIPROT_DG	10802664, 11726611		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CORNEA PLANA 2	Cornea Plana	GENOMICS_ENGLAND_DG	10802664, 23834557		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cornea Plana 2	Cornea plana	Pubtator	26099342, 31059048	Associate	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CORNEA PLANA 2	Cornea Plana	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CORNEA PLANA 2	Cornea Plana	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Drusen	Drusen	BEFREE	30404605		★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	BEFREE	12975606		★☆☆☆☆ Found in Text Mining only
Glycogen storage disease type II	Glycogen Storage Disease	BEFREE	30404605		★☆☆☆☆ Found in Text Mining only
Hyperopia	Hyperopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	BEFREE	11683372		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	Pubtator	11683372	Stimulate	★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	Pubtator	23727491	Associate	★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	BEFREE	29760442		★☆☆☆☆ Found in Text Mining only
Primary angle-closure glaucoma	Angle closure glaucoma	BEFREE	25967529		★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	BEFREE	16490510, 21743019		★☆☆☆☆ Found in Text Mining only