KLF3
KLF transcription factor 3, the group of Kruppel like factors|Zinc fingers C2H2-type
Basic information
Region (hg38): 4:38664197-38701517
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 KLF3 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 | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in KLF3
This is a list of pathogenic ClinVar variants found in the KLF3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-38680644-G-C | not specified | Uncertain significance (Aug 08, 2022) | ||
| 4-38688649-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 4-38688744-C-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| 4-38688787-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 4-38688793-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| 4-38688852-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
| 4-38688867-G-A | not specified | Uncertain significance (Jun 11, 2024) | ||
| 4-38688940-G-C | not specified | Uncertain significance (Jun 23, 2021) | ||
| 4-38689797-C-T | not specified | Uncertain significance (Jan 04, 2022) | ||
| 4-38689833-C-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 4-38694751-A-G | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 4-38694908-T-C | not provided (-) | |||
| 4-38697192-C-T | not specified | Uncertain significance (Sep 26, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KLF3 | protein_coding | protein_coding | ENST00000261438 | 5 | 36847 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.830 | 0.170 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.55 | 148 | 212 | 0.699 | 0.0000127 | 2247 |
| Missense in Polyphen | 24 | 67.217 | 0.35705 | 696 | ||
| Synonymous | -0.121 | 87 | 85.6 | 1.02 | 0.00000580 | 685 |
| Loss of Function | 3.06 | 2 | 14.6 | 0.137 | 7.00e-7 | 187 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000186 | 0.000185 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the CACCC box of erythroid cell-expressed genes. May play a role in hematopoiesis (By similarity). {ECO:0000250}.;
- Pathway
- Transcriptional misregulation in cancer - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.207
- rvis_EVS
- -0.74
- rvis_percentile_EVS
- 13.94
Haploinsufficiency Scores
- pHI
- 0.231
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.624
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Klf3
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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; respiratory system phenotype; liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- klf3
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;multicellular organism development;cellular response to peptide
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;metal ion binding