KRT18
keratin 18, the group of Keratins, type I
Basic information
Region (hg38): 12:52948871-52952906
Links
Phenotypes
GenCC
Source:
- cirrhosis, familial (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (31 variants)
- not_provided (18 variants)
- Hepatitis_C_virus,_susceptibility_to (3 variants)
- Cirrhosis,_familial (3 variants)
- Cirrhosis,_noncryptogenic,_susceptibility_to (1 variants)
- Cirrhosis,_cryptogenic (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT18 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000224.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 43 | 45 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 46 | 2 | 1 |
Highest pathogenic variant AF is 0.00032159
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KRT18 | protein_coding | protein_coding | ENST00000388835 | 7 | 4031 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.735 | 0.265 | 125697 | 0 | 3 | 125700 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 202 | 248 | 0.815 | 0.0000152 | 2776 |
| Missense in Polyphen | 14 | 22.33 | 0.62696 | 429 | ||
| Synonymous | -0.488 | 109 | 103 | 1.06 | 0.00000595 | 870 |
| Loss of Function | 3.21 | 3 | 17.5 | 0.171 | 9.46e-7 | 194 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the uptake of thrombin-antithrombin complexes by hepatic cells (By similarity). When phosphorylated, plays a role in filament reorganization. Involved in the delivery of mutated CFTR to the plasma membrane. Together with KRT8, is involved in interleukin-6 (IL-6)-mediated barrier protection. {ECO:0000250, ECO:0000269|PubMed:15529338, ECO:0000269|PubMed:16424149, ECO:0000269|PubMed:17213200, ECO:0000269|PubMed:7523419, ECO:0000269|PubMed:8522591, ECO:0000269|PubMed:9298992, ECO:0000269|PubMed:9524113}.;
- Disease
- DISEASE: Cirrhosis (CIRRH) [MIM:215600]: A liver disease characterized by severe panlobular liver-cell swelling with Mallory body formation, prominent pericellular fibrosis, and marked deposits of copper. Clinical features include abdomen swelling, jaundice and pulmonary hypertension. {ECO:0000269|PubMed:12724528, ECO:0000269|PubMed:9011570}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Estrogen signaling pathway - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Pathogenic Escherichia coli infection;Keratinization;Developmental Biology;EGFR1;Caspase Cascade in Apoptosis
(Consensus)
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- loftool
- 0.0333
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.516
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Krt18
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; embryo phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- cell cycle;anatomical structure morphogenesis;viral process;keratinization;tumor necrosis factor-mediated signaling pathway;Golgi to plasma membrane CFTR protein transport;negative regulation of apoptotic process;intermediate filament cytoskeleton organization;cornification;extrinsic apoptotic signaling pathway;hepatocyte apoptotic process;cell-cell adhesion
- Cellular component
- nucleolus;cytoplasm;microtubule organizing center;cytosol;intermediate filament;cell-cell adherens junction;centriolar satellite;keratin filament;perinuclear region of cytoplasm;extracellular exosome;cell periphery
- Molecular function
- RNA binding;structural molecule activity;protein binding;scaffold protein binding;cadherin binding involved in cell-cell adhesion