KERA

gene
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Also known as SLRR2B

Summary

KERA (keratocan, HGNC:6309) is a protein-coding gene on chromosome 12q21.33, encoding Keratocan (O60938). May be important in developing and maintaining corneal transparency and for the structure of the stromal matrix.

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).

Source: NCBI Gene 11081 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cornea plana (Definitive, GenCC) — +2 more curated relationships
  • GWAS associations: 4
  • Clinical variants (ClinVar): 97 total — 10 pathogenic, 4 likely-pathogenic
  • Phenotypes (HPO): 10
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_007035

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6309
Approved symbolKERA
Namekeratocan
Location12q21.33
Locus typegene with protein product
StatusApproved
AliasesSLRR2B
Ensembl geneENSG00000139330
Ensembl biotypeprotein_coding
OMIM603288
Entrez11081

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000266719

RefSeq mRNA: 1 — MANE Select: NM_007035 NM_007035

CCDS: CCDS9037

Canonical transcript exons

ENST00000266719 — 3 exons

ExonStartEnd
ENSE000011431659105774491058024
ENSE000011514539105049191051518
ENSE000013809949105539691056289

Expression profiles

Bgee: expression breadth broad, 85 present calls, max score 89.49.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4317 / max 160.6761, expressed in 26 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
1325370.231021
1325410.065512
1325340.03479
1325390.026610
1325360.02316
1325420.01718
1325380.016010
1325400.01155
1325350.00624

Top tissues by expression

274 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370189.49gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.10gold quality
tendonUBERON:000004378.06gold quality
cartilage tissueUBERON:000241877.70gold quality
synovial jointUBERON:000221762.75gold quality
tendon of biceps brachiiUBERON:000818860.76silver quality
layer of synovial tissueUBERON:000761660.51silver quality
gall bladderUBERON:000211060.33gold quality
lower lobe of lungUBERON:000894956.63silver quality
tibialis anteriorUBERON:000138555.30silver quality
tracheaUBERON:000312654.20silver quality
penisUBERON:000098953.67silver quality
hair follicleUBERON:000207353.28gold quality
urethraUBERON:000005753.16silver quality
ileal mucosaUBERON:000033152.17silver quality
superior surface of tongueUBERON:000737150.71silver quality
thoracic mammary glandUBERON:000520050.51gold quality
mammary glandUBERON:000191150.35gold quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
blood vessel layerUBERON:000479749.29gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
epithelial cell of pancreasCL:000008349.09gold quality
olfactory bulbUBERON:000226448.92gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
oviduct epitheliumUBERON:000480448.72gold quality
vastus lateralisUBERON:000137948.68gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting KERA, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-428299.9975.366408
HSA-MIR-607799.9968.042299
HSA-MIR-480399.9871.993117
HSA-MIR-56899.9869.862084
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-211099.9666.681930
HSA-MIR-365899.9673.874379
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-568099.9169.833421
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-367199.9073.043897
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-313399.8170.923506
HSA-MIR-4760-5P99.8069.881619
HSA-MIR-5002-5P99.7670.841763
HSA-MIR-425599.7267.701541
HSA-MIR-117999.7168.701040
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-472999.6972.184233
HSA-MIR-58699.6570.402051
HSA-MIR-10393-5P99.6568.011368
HSA-MIR-570099.6469.882280
HSA-MIR-205399.5769.151635
HSA-MIR-1211799.5067.57868
HSA-MIR-513C-5P99.5068.421730
HSA-MIR-514B-5P99.5068.191766
HSA-MIR-312899.5067.851258

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 14)

  • KERA mutation is associated with autosomal recessive cornea plana (PMID:15370545)
  • This is the first report of the identification of a mutation within KERA in a family of Hispanic origin with autosomal recessive cornea plana. (PMID:16157807)
  • No evidence that endothelial dysfunction and germline mutation of lumican and keratocan genes participate in the etiology of subepithelial corneal haze. (PMID:16760896)
  • Specific for mutation in KERA, the ophthalmic phenotype of recessive cornea plana does not significantly vary with different KERA mutations. (PMID:17011957)
  • In addition, no pathogenic sequence variations were found in DCN, DSPG3, LUM, PITX2 and FOXC1, which have also been implicated in corneal and anterior segment dysgenesis. (PMID:17558846)
  • This is the first description of recessive cornea plana in a white British family and it is the second report on the p.N247S change in the KERA gene. (PMID:17679937)
  • Multiple core-protein species were detected for decorin, biglycan, lumican and keratocan in the degenerate osteoarthritic articular cartilage and menisci. (PMID:18620607)
  • Linkage and haplotype analyses identified 12q21.33 as a locus for posterior amorphous corneal dystrophy. However, no mutations were identified in the candidate genes (KERA, LUM, DCN, EPYC) within this region. (PMID:20357198)
  • Corneal endothelial disorders were found with compound mutations in KERA (PMID:23834557)
  • rare variant in KERA was identified in a large kindred with premature atherosclerosis (PMID:24879339)
  • The mutation that we report here leads to the deletion of a conserved amino acid (p.Phe125del) from the third LRR motif of the keratocan protein, which might lead to an abnormal tertiary structure of the protein, thereby leading to the disease. (PMID:25967529)
  • a novel KERA variant, p.(Ile225Thr), was detected that segregates with Cornea plana in the homozygous form. (PMID:26099342)
  • KERA mutation c.740A>G has been identified to date in three different populations, which makes it the most frequently occurring mutation in patients with cornea plana (PMID:28677912)
  • We expand the phenotypic spectrum of biallelic KERA mutations in this report of a boy with juvenile corneal ectasia who was found to harbor an underlying novel homozygous mutation in the gene. (PMID:28799822)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriokeraENSDARG00000056938
mus_musculusKeraENSMUSG00000019932
rattus_norvegicusKeraENSRNOG00000004635

Paralogs (10): EPYC (ENSG00000083782), OGN (ENSG00000106809), ECM2 (ENSG00000106823), FMOD (ENSG00000122176), OMG (ENSG00000126861), OMD (ENSG00000127083), LUM (ENSG00000139329), PRELP (ENSG00000188783), LINGO4 (ENSG00000213171), LINGO3 (ENSG00000220008)

Protein

Protein identifiers

KeratocanO60938 (reviewed: O60938)

Alternative names: Keratan sulfate proteoglycan keratocan

All UniProt accessions (1): O60938

UniProt curated annotations — full annotation on UniProt →

Function. May be important in developing and maintaining corneal transparency and for the structure of the stromal matrix.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Cornea (at protein level). Increased expression in the stroma of keratoconus corneas. Also detected in trachea, and in low levels, in intestine, skeletal muscle, ovary, lung and putamen.

Post-translational modifications. Binds keratan sulfate chains.

Disease relevance. Cornea plana 2, autosomal recessive (CNA2) [MIM:217300] A severe form of cornea plana, a rare ocular disorder characterized by flattened corneal curvature leading to a decrease in refraction, reduced visual activity, hyperopia, hazy corneal limbus, opacities in the corneal parenchyma, and marked arcus senilis often detected at an early age. CNA2 patients manifest extreme hyperopia and additional ocular anomalies such as malformations of the iris, a slit-like pupil, and adhesions between iris and cornea. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class II subfamily.

RefSeq proteins (1): NP_008966* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000372LRRNTDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR050333SLRPFamily

Pfam: PF01462, PF13516, PF13855

UniProt features (23 total): repeat 10, glycosylation site 4, disulfide bond 3, sequence variant 3, signal peptide 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O60938-F187.420.75

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (3): 42–48, 46–58, 303–343

Glycosylation sites (4): 93, 167, 222, 298

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

IDPathway
R-HSA-2022854Keratan sulfate biosynthesis
R-HSA-2022857Keratan sulfate degradation
R-HSA-3656225Defective CHST6 causes MCDC1
R-HSA-3656243Defective ST3GAL3 causes MCT12 and EIEE15
R-HSA-3656244Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)
R-HSA-1430728Metabolism
R-HSA-1630316Glycosaminoglycan metabolism
R-HSA-1638074Keratan sulfate/keratin metabolism
R-HSA-1643685Disease
R-HSA-3560782Diseases associated with glycosaminoglycan metabolism
R-HSA-3781865Diseases of glycosylation
R-HSA-5668914Diseases of metabolism
R-HSA-71387Metabolism of carbohydrates and carbohydrate derivatives

MSigDB gene sets: 104 (showing top): TAL1ALPHAE47_01, MARTINEZ_RB1_TARGETS_DN, YY1_02, chr12q21, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, TGGNNNNNNKCCAR_UNKNOWN, GOBP_SENSORY_PERCEPTION, GOBP_SENSORY_ORGAN_DEVELOPMENT, SOX5_01, NKX3A_01, TAL1BETAE47_01, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, TGGAAA_NFAT_Q4_01, GOCC_LYSOSOMAL_LUMEN, GOCC_VACUOLAR_LUMEN

GO Biological Process (2): visual perception (GO:0007601), cornea development in camera-type eye (GO:0061303)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), Golgi lumen (GO:0005796), extracellular matrix (GO:0031012), lysosomal lumen (GO:0043202)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Diseases associated with glycosaminoglycan metabolism3
Keratan sulfate/keratin metabolism2
Metabolism of carbohydrates and carbohydrate derivatives1
Glycosaminoglycan metabolism1
Diseases of glycosylation1
Diseases of metabolism1
Disease1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
sensory perception of light stimulus1
camera-type eye development1
anatomical structure development1
binding1
cellular anatomical structure1
Golgi apparatus1
intracellular organelle lumen1
external encapsulating structure1
lysosome1
vacuolar lumen1

Protein interactions and networks

STRING

1146 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KERACXCL1P09341839
KERAPPP3CAQ08209800
KERAALDH3A1P30838760
KERACHST6Q9GZX3728
KERACHST1O43916727
KERACHST3Q7LGC8691
KERAKRT12Q99456680
KERAOGNP20774626
KERAACANP16112605
KERASULT1C3Q6IMI6602
KERASULT1C4O75897599
KERASULT1B1O43704595
KERAKRT3P12035595
KERACACNA1FO60840591
KERAB3GNT7Q8NFL0590

IntAct

7 interactions, top by confidence:

ABTypeScore
EMILIN1METTL15psi-mi:“MI:0914”(association)0.530
KERAFBXO21psi-mi:“MI:0914”(association)0.530
KERADlg4psi-mi:“MI:0407”(direct interaction)0.440
CDC37KERApsi-mi:“MI:0915”(physical association)0.400
KERAVWA8psi-mi:“MI:0914”(association)0.350

BioGRID (31): NUDT12 (Affinity Capture-MS), CNPY4 (Affinity Capture-MS), VWA8 (Affinity Capture-MS), EID2 (Affinity Capture-MS), FBXO21 (Affinity Capture-MS), BLMH (Affinity Capture-MS), SQSTM1 (Affinity Capture-MS), MAP3K7 (Affinity Capture-MS), B4GALT5 (Affinity Capture-MS), PRKCI (Affinity Capture-MS), STK11IP (Affinity Capture-MS), LRRC40 (Affinity Capture-MS), ABHD14A (Affinity Capture-MS), KERA (Positive Genetic), ITIH2 (Affinity Capture-MS)

ESM2 similar proteins: C0STK7, C3YZ59, O00206, O15455, O42235, O60938, O62702, O93233, P58727, Q0PV50, Q2V898, Q45R42, Q58A48, Q5BK65, Q5M7S9, Q5TJ59, Q62192, Q65YW8, Q65Z91, Q68Y56, Q6AXL3, Q6DF55, Q6R5N8, Q6R5P0, Q7Z2Q7, Q80X72, Q8BMT4, Q8BZT5, Q8C031, Q8N6Y2, Q8R5M3, Q8SPE8, Q8SPE9, Q965M2, Q99467, Q99MB1, Q99PH1, Q9CQ76, Q9CXD9, Q9DE66

Diamond homologs: A3KNN3, A6H789, A6H793, A6NJW4, A8WHP9, E7FE13, F1MLX5, G5EFX6, O02678, O02833, O35367, O46378, O46379, O46542, O60938, O62702, O75093, O75094, O88279, O88280, O94813, P07359, P07585, P21793, P24014, P28654, P28675, P35858, P35859, P51884, P51885, P51886, P51888, P51890, P58874, P59034, P59035, P70186, P70389, P83286

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

97 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic10
Likely pathogenic4
Uncertain significance55
Likely benign15
Benign5

Top pathogenic / likely-pathogenic (14)

Variant IDHGVSClassification
1940458NM_007035.4(KERA):c.55_56del (p.Trp19fs)Pathogenic
225521NM_007035.4(KERA):c.320T>G (p.Ile107Arg)Pathogenic
2735921NM_007035.4(KERA):c.209C>T (p.Pro70Leu)Pathogenic
3609569NM_007035.4(KERA):c.809C>A (p.Ser270Ter)Pathogenic
4767828NM_007035.4(KERA):c.748_757del (p.Ser250fs)Pathogenic
56550NM_007035.4(KERA):c.835C>T (p.Arg279Ter)Pathogenic
6519NM_007035.4(KERA):c.740A>G (p.Asn247Ser)Pathogenic
6520NM_007035.4(KERA):c.520C>T (p.Gln174Ter)Pathogenic
6521NM_007035.4(KERA):c.644C>A (p.Thr215Lys)Pathogenic
6522NM_007035.4(KERA):c.937C>T (p.Arg313Ter)Pathogenic
3779786NM_007035.4(KERA):c.242A>G (p.Asn81Ser)Likely pathogenic
4087749NM_007035.4(KERA):c.38_41del (p.Leu12_Phe13insTer)Likely pathogenic
4531440NM_007035.4(KERA):c.528C>G (p.Asn176Lys)Likely pathogenic
56549NM_007035.4(KERA):c.391A>G (p.Asn131Asp)Likely pathogenic

SpliceAI

281 predictions. Top by Δscore:

VariantEffectΔscore
12:91051514:CACAC:Cacceptor_gain0.9900
12:91051516:CAC:Cacceptor_gain0.9900
12:91051517:ACCTA:Aacceptor_loss0.9900
12:91051519:CT:Cacceptor_loss0.9900
12:91051520:T:Aacceptor_loss0.9900
12:91055394:A:ACdonor_gain0.9900
12:91055395:C:CCdonor_gain0.9900
12:91056289:CCTA:Cacceptor_loss0.9900
12:91056290:C:CGacceptor_loss0.9900
12:91056291:T:Aacceptor_loss0.9900
12:91055390:ACTT:Adonor_loss0.9800
12:91055391:CT:Cdonor_loss0.9800
12:91055392:TT:Tdonor_loss0.9800
12:91055393:TA:Tdonor_loss0.9800
12:91055394:AC:Adonor_loss0.9800
12:91055395:C:CTdonor_loss0.9800
12:91055395:CT:Cdonor_gain0.9800
12:91056287:CAC:Cacceptor_gain0.9800
12:91056290:C:CCacceptor_gain0.9800
12:91051519:C:CCacceptor_gain0.9700
12:91055387:GTTAC:Gdonor_loss0.9700
12:91055388:TTACT:Tdonor_loss0.9700
12:91055389:TAC:Tdonor_loss0.9700
12:91057747:G:Adonor_gain0.9700
12:91057804:A:Tacceptor_gain0.9600
12:91057955:GCTTA:Gdonor_loss0.9600
12:91057956:CTTA:Cdonor_loss0.9600
12:91057957:TTACC:Tdonor_loss0.9600
12:91057958:TA:Tdonor_loss0.9600
12:91057959:A:AGdonor_loss0.9600

AlphaMissense

2332 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:91055482:A:GL267P0.998
12:91055764:A:GL173P0.998
12:91055770:A:TL171H0.998
12:91055826:A:CN152K0.998
12:91055826:A:TN152K0.998
12:91055827:T:AN152I0.998
12:91055842:A:GL147S0.998
12:91055889:A:CN131K0.998
12:91055889:A:TN131K0.998
12:91055914:A:CL123W0.998
12:91055967:G:CN105K0.998
12:91055967:G:TN105K0.998
12:91055968:T:AN105I0.998
12:91055969:T:AN105Y0.998
12:91055977:A:GL102P0.998
12:91056108:A:CC58W0.998
12:91056109:C:TC58Y0.998
12:91055422:A:GL287P0.997
12:91055466:A:CN272K0.997
12:91055466:A:TN272K0.997
12:91055476:A:GL269P0.997
12:91055551:A:GL244P0.997
12:91055770:A:GL171P0.997
12:91055779:A:GL168P0.997
12:91055828:T:AN152Y0.997
12:91055890:T:AN131I0.997
12:91055891:T:AN131Y0.997
12:91056039:G:CN81K0.997
12:91056039:G:TN81K0.997
12:91056049:A:GL78P0.997

dbSNP variants (sampled 300 via entrez): RS1000377132 (12:91054076 A>G), RS1000679087 (12:91052293 G>C,T), RS1000828568 (12:91058809 G>A,C), RS1001290845 (12:91056635 C>T), RS1001574220 (12:91054887 C>T), RS1002270095 (12:91059657 T>A), RS1002408949 (12:91059348 G>A), RS1002942726 (12:91059616 T>C), RS1002994160 (12:91053587 C>T), RS1003210732 (12:91054431 C>G,T), RS1003288601 (12:91053783 T>A), RS1003590589 (12:91054133 C>T), RS1003725500 (12:91058241 G>A,T), RS1003844265 (12:91052858 T>A,G), RS1004325815 (12:91053401 T>C,G)

Disease associations

OMIM: gene MIM:603288 | disease phenotypes: MIM:217300

GenCC curated gene-disease

DiseaseClassificationInheritance
cornea planaDefinitiveAutosomal recessive
cornea plana 2StrongAutosomal recessive
congenital cornea planaSupportiveAutosomal dominant

Mondo (3): cornea plana 2 (MONDO:0009014), (MONDO:0018888), cornea plana (MONDO:0000733)

Orphanet (1): Congenital cornea plana (Orphanet:53691)

HPO phenotypes

10 total (10 of 10 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000540Hypermetropia
HP:0000568Microphthalmia
HP:0000647Sclerocornea
HP:0001084Corneal arcus
HP:0007663Reduced visual acuity
HP:0007720Flat cornea
HP:0007957Corneal opacity
HP:0011463Childhood onset
HP:0100689Decreased corneal thickness

GWAS associations

4 associations (top):

StudyTraitp-value
GCST001784_42Pulmonary function (smoking interaction)5.000000e-07
GCST002307_11Systolic blood pressure (alcohol consumption interaction)2.000000e-07
GCST002307_4Systolic blood pressure (alcohol consumption interaction)2.000000e-07
GCST008758_18Pre-treatment viral load in HIV-1 infection8.000000e-17

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0003892pulmonary function measurement
EFO:0004713FEV/FVC ratio
EFO:0004329alcohol drinking
EFO:0006335systolic blood pressure
EFO:0010125viral load

MeSH disease descriptors (1)

DescriptorNameTree numbers
C565677Cornea Plana 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

ChemicalActions (top 5)PubMed papers
2-palmitoylglycerolincreases expression1
Vorinostatincreases expression1
Benzo(a)pyrenedecreases methylation, increases methylation1
Valproic Acidaffects expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.