KLF4
KLF transcription factor 4, the group of Kruppel like factors|Zinc fingers C2H2-type
Basic information
Region (hg38): 9:107484851-107490482
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF4 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 | 11 | |||||
| missense | 28 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 28 | 13 | 3 |
Variants in KLF4
This is a list of pathogenic ClinVar variants found in the KLF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-107485787-C-T | KLF4-related disorder | Benign/Likely benign (Dec 04, 2023) | ||
| 9-107487103-T-A | KLF4-related disorder | Uncertain significance (Jan 26, 2024) | ||
| 9-107487113-G-A | KLF4-related disorder | Likely benign (Dec 21, 2020) | ||
| 9-107487134-T-C | KLF4-related disorder | Benign (Dec 31, 2019) | ||
| 9-107487169-T-C | not specified | Uncertain significance (Dec 26, 2023) | ||
| 9-107487177-C-G | not specified | Uncertain significance (Oct 12, 2021) | ||
| 9-107487179-G-A | KLF4-related disorder | Benign/Likely benign (Mar 25, 2019) | ||
| 9-107487199-G-T | KLF4-related disorder | Benign (Jan 20, 2020) | ||
| 9-107487309-G-C | not specified | Uncertain significance (Aug 17, 2021) | ||
| 9-107487335-G-C | Likely benign (Jun 05, 2018) | |||
| 9-107487340-G-C | not specified | Uncertain significance (Jun 10, 2024) | ||
| 9-107487421-G-A | KLF4-related disorder | Benign/Likely benign (Sep 30, 2021) | ||
| 9-107487424-C-A | not specified | Likely benign (Jun 06, 2023) | ||
| 9-107487493-C-G | not specified | Likely benign (Nov 07, 2023) | ||
| 9-107487510-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
| 9-107487522-C-A | not specified | Uncertain significance (Mar 07, 2023) | ||
| 9-107487535-G-A | KLF4-related disorder | Likely benign (Aug 04, 2020) | ||
| 9-107487573-C-T | not specified | Uncertain significance (Oct 02, 2023) | ||
| 9-107487615-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 9-107487615-G-C | not specified | Uncertain significance (Aug 09, 2021) | ||
| 9-107487627-T-C | not specified | Uncertain significance (Jan 25, 2023) | ||
| 9-107487627-TCAGGGCTGCCTTTGCTGACGCTGATGACCGACGGGCTGCCGTACTCGCTGC-T | KLF4-related disorder | Likely benign (Jul 31, 2020) | ||
| 9-107487679-C-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 9-107487703-G-A | Likely benign (Dec 31, 2019) | |||
| 9-107487712-T-G | not specified | Uncertain significance (Oct 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KLF4 | protein_coding | protein_coding | ENST00000374672 | 5 | 5631 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00286 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.100 | 275 | 280 | 0.983 | 0.0000147 | 3020 |
| Missense in Polyphen | 127 | 143.63 | 0.88421 | 1537 | ||
| Synonymous | -2.43 | 163 | 128 | 1.27 | 0.00000749 | 1025 |
| Loss of Function | 3.84 | 0 | 17.2 | 0.00 | 9.43e-7 | 177 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor; can act both as activator and as repressor. Binds the 5'-CACCC-3' core sequence. Binds to the promoter region of its own gene and can activate its own transcription. Regulates the expression of key transcription factors during embryonic development. Plays an important role in maintaining embryonic stem cells, and in preventing their differentiation. Required for establishing the barrier function of the skin and for postnatal maturation and maintenance of the ocular surface. Involved in the differentiation of epithelial cells and may also function in skeletal and kidney development. Contributes to the down-regulation of p53/TP53 transcription. {ECO:0000269|PubMed:17308127, ECO:0000269|PubMed:20071344}.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);SRF and miRs in Smooth Muscle Differentiation and Proliferation;Cell Differentiation - Index expanded;White fat cell differentiation;Mesodermal Commitment Pathway;Vitamin D Receptor Pathway;let-7 inhibition of ES cell reprogramming;Preimplantation Embryo;Role of Osx and miRNAs in tooth development;White fat cell differentiation;Developmental Biology;Transcriptional regulation of pluripotent stem cells;Regulation of nuclear beta catenin signaling and target gene transcription
(Consensus)
Recessive Scores
- pRec
- 0.408
Intolerance Scores
- loftool
- rvis_EVS
- -0.45
- rvis_percentile_EVS
- 24.19
Haploinsufficiency Scores
- pHI
- 0.840
- hipred
- Y
- hipred_score
- 0.857
- ghis
- 0.573
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.956
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Klf4
- Phenotype
- neoplasm; hematopoietic system phenotype; reproductive system 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- klf4
- Affected structure
- goblet cell
- Phenotype tag
- abnormal
- Phenotype quality
- poorly differentiated
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;mesodermal cell fate determination;negative regulation of cell population proliferation;epidermal cell differentiation;positive regulation of gene expression;negative regulation of gene expression;negative regulation of phosphatidylinositol 3-kinase signaling;negative regulation of muscle hyperplasia;negative regulation of angiogenesis;stem cell population maintenance;post-embryonic camera-type eye development;negative regulation of NF-kappaB transcription factor activity;positive regulation of cellular protein metabolic process;negative regulation of heterotypic cell-cell adhesion;somatic stem cell population maintenance;post-embryonic hemopoiesis;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;regulation of phosphatidylinositol 3-kinase activity;negative regulation of interleukin-8 biosynthetic process;positive regulation of nitric oxide biosynthetic process;fat cell differentiation;regulation of cell differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of hemoglobin biosynthetic process;negative regulation of smooth muscle cell proliferation;regulation of axon regeneration;epidermis morphogenesis;negative regulation of inflammatory response;positive regulation of protein metabolic process;negative regulation of protein kinase B signaling;positive regulation of telomerase activity;canonical Wnt signaling pathway;negative regulation of response to cytokine stimulus;pri-miRNA transcription by RNA polymerase II;cellular response to hydrogen peroxide;negative regulation of ERK1 and ERK2 cascade;cellular response to retinoic acid;cellular response to growth factor stimulus;cellular response to cycloheximide;cellular response to laminar fluid shear stress;negative regulation of cell migration involved in sprouting angiogenesis;cellular response to peptide;positive regulation of sprouting angiogenesis;positive regulation of core promoter binding;negative regulation of leukocyte adhesion to arterial endothelial cell;cellular response to leukemia inhibitory factor;negative regulation of G1/S transition of mitotic cell cycle;negative regulation of chemokine (C-X-C motif) ligand 2 production
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;nuclear euchromatin;cytoplasm;nuclear transcription factor complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity;RNA polymerase II transcription factor binding;transcription cofactor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;beta-catenin binding;zinc ion binding;phosphatidylinositol 3-kinase regulator activity;histone deacetylase binding;transcription regulatory region DNA binding;promoter-specific chromatin binding