KERA

keratocan, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 12:91050490-91058024

Previous symbols: [ "CNA2" ]

Links

ENSG00000139330 ∙ NCBI:11081 ∙ OMIM:603288 ∙ HGNC:6309 ∙ Uniprot:O60938 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cornea plana 2 (Strong), mode of inheritance: AR
• congenital cornea plana (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cornea plana 2, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	10802664; 11726611; 15370545; 17679937

ClinVar

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

• not provided (17 variants)
• Inborn genetic diseases (12 variants)
• Cornea plana 2 (6 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KERA 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				4	4	8
missense	1		16	2		19
nonsense	1					1
start loss						0
frameshift	1	1				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	3	1	16	7	4

Highest pathogenic variant AF is 0.0000397

Variants in KERA

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

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

Position	Type	Phenotype	Significance	ClinVar
12-91051360-C-G		not specified	Uncertain significance (Mar 07, 2023)
12-91051378-AG-A		Cornea plana 2	Conflicting classifications of pathogenicity (Mar 26, 2024)
12-91051437-C-T		not specified	Uncertain significance (Apr 25, 2022)
12-91051438-G-A		not specified	Uncertain significance (Aug 04, 2023)
12-91051467-C-T			Likely benign (Jul 18, 2023)
12-91051468-G-A		Cornea plana 2	Pathogenic (Jun 01, 2004)
12-91051498-A-G		not specified	Uncertain significance (Aug 17, 2021)
12-91051526-G-A			Benign (Jan 31, 2024)
12-91055446-C-T			Likely benign (May 17, 2023)
12-91055447-G-A		Cornea plana 2	Pathogenic (Dec 22, 2022)
12-91055485-T-C		not specified	Uncertain significance (Jan 19, 2024)
12-91055542-T-C		Cornea plana 2	Pathogenic (Jan 01, 2002)
12-91055543-T-C			Uncertain significance (Feb 05, 2023)
12-91055553-T-C			Likely benign (Jul 01, 2022)
12-91055563-G-A		not specified	Uncertain significance (Jun 06, 2023)
12-91055563-G-T			Uncertain significance (Aug 12, 2022)
12-91055586-A-C			Pathogenic (Oct 03, 2023)
12-91055622-T-C			Likely benign (Feb 01, 2023)
12-91055638-G-T		Cornea plana 2	Pathogenic (Dec 01, 2001)
12-91055659-G-C		Cornea plana 2	Uncertain significance (May 22, 2022)
12-91055661-C-T		not specified	Uncertain significance (Jun 03, 2022)
12-91055665-T-A		not specified	Uncertain significance (May 11, 2022)
12-91055667-C-T			Likely benign (Sep 29, 2023)
12-91055698-A-G		not specified	Uncertain significance (Jan 03, 2024)
12-91055728-C-T		not specified	Uncertain significance (Apr 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KERA	protein_coding	protein_coding	ENST00000266719	2	7493

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-7	0.245	125545	0	38	125583	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.324	191	179	1.07	0.00000837	2324
Missense in Polyphen		42	42.629	0.98525		593
Synonymous	-1.27	79	65.8	1.20	0.00000312	673
Loss of Function	0.305	11	12.1	0.906	7.01e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000447
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be important in developing and maintaining corneal transparency and for the structure of the stromal matrix. {ECO:0000305|PubMed:10802664, ECO:0000305|PubMed:11726611}.
• Disease: DISEASE: 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. {ECO:0000269|PubMed:10802664, ECO:0000269|PubMed:11726611}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Metabolism;Integrin (Consensus)

Recessive Scores

• pRec: 0.265

Intolerance Scores

• loftool: 0.598
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.0988
• hipred: N
• hipred_score: 0.394
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kera
• Phenotype: immune system phenotype; hematopoietic system phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: kera
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: visual perception;keratan sulfate biosynthetic process;keratan sulfate catabolic process;response to stimulus;cornea development in camera-type eye
• Cellular component: extracellular region;Golgi lumen;extracellular matrix;lysosomal lumen
• Molecular function: molecular_function