KERA
Basic information
Region (hg38): 12:91050491-91058024
Previous symbols: [ "CNA2" ]
Links
Phenotypes
GenCC
Source:
- cornea plana 2 (Strong), mode of inheritance: AR
- congenital cornea plana (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
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
- not provided (4 variants)
- Cornea plana 2 (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 | 10 | |||||
missense | 21 | 25 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 1 | |||||
Total | 4 | 1 | 21 | 10 | 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 (Sep 22, 2024) | ||
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) | |||
12-91055693-G-C | not specified | Uncertain significance (Jun 04, 2024) | ||
12-91055698-A-G | not specified | Uncertain significance (Jan 03, 2024) |
GnomAD
Source:
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:
- 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