KLF9
Basic information
Region (hg38): 9:70384604-70414657
Previous symbols: [ "BTEB1" ]
Links
Phenotypes
GenCC
Source:
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 KLF9 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 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 0 |
Variants in KLF9
This is a list of pathogenic ClinVar variants found in the KLF9 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-70387820-T-C | not specified | Uncertain significance (Jun 18, 2024) | ||
| 9-70387846-G-C | not specified | Uncertain significance (Dec 09, 2023) | ||
| 9-70413086-A-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| 9-70413217-G-C | not specified | Uncertain significance (Dec 15, 2023) | ||
| 9-70413222-C-G | not specified | Uncertain significance (Oct 19, 2024) | ||
| 9-70413237-C-T | not specified | Uncertain significance (May 13, 2024) | ||
| 9-70413240-C-G | not specified | Uncertain significance (Oct 19, 2024) | ||
| 9-70413273-G-T | not specified | Uncertain significance (Feb 13, 2025) | ||
| 9-70413278-A-C | not specified | Likely benign (Apr 07, 2023) | ||
| 9-70413284-T-A | not specified | Uncertain significance (Apr 17, 2023) | ||
| 9-70413300-C-A | not specified | Uncertain significance (Jan 22, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KLF9 | protein_coding | protein_coding | ENST00000377126 | 2 | 30038 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.888 | 0.111 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.27 | 75 | 154 | 0.486 | 0.00000897 | 1584 |
| Missense in Polyphen | 10 | 54.078 | 0.18492 | 529 | ||
| Synonymous | 0.970 | 56 | 66.0 | 0.848 | 0.00000375 | 492 |
| Loss of Function | 2.47 | 0 | 7.11 | 0.00 | 3.03e-7 | 88 |
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 that binds to GC box promoter elements. Selectively activates mRNA synthesis from genes containing tandem repeats of GC boxes but represses genes with a single GC box. Acts as an epidermal circadian transcription factor regulating keratinocyte proliferation (PubMed:22711835). {ECO:0000269|PubMed:22711835}.;
- Pathway
- Exercise-induced Circadian Regulation
(Consensus)
Recessive Scores
- pRec
- 0.174
Intolerance Scores
- loftool
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 73.97
Haploinsufficiency Scores
- pHI
- 0.994
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.483
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Klf9
- Phenotype
- homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- klf9
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;circadian rhythm;negative regulation of keratinocyte proliferation;cellular response to cortisol stimulus;cellular response to thyroid hormone stimulus
- Cellular component
- nucleus;nucleoplasm;cytosol;plasma membrane
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;metal ion binding