KLF11

KLF transcription factor 11, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 2:10042848-10054836

Previous symbols: [ "TIEG2" ]

Links

ENSG00000172059 ∙ NCBI:8462 ∙ OMIM:603301 ∙ HGNC:11811 ∙ Uniprot:O14901 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• maturity-onset diabetes of the young (Supportive), mode of inheritance: AD
• maturity-onset diabetes of the young type 7 (Strong), mode of inheritance: AD
• monogenic diabetes (Refuted Evidence), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Maturity-onset diabetes of the young, type VII	AD	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	Endocrine	15774581

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLF11 gene.

• Maturity-onset diabetes of the young type 7 (111 variants)
• not provided (97 variants)
• Inborn genetic diseases (22 variants)
• not specified (19 variants)
• Monogenic diabetes (8 variants)
• Maturity onset diabetes mellitus in young (7 variants)
• KLF11-related condition (4 variants)
• Diabetes mellitus (1 variants)
• Hyperglycemia;Maturity onset diabetes mellitus in young (1 variants)
• Type 2 diabetes mellitus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF11 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			3	18	4	25
missense			74	14	1	89
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			1		1	2
non coding			39	18	25	82
Total	0	0	119	50	30

Variants in KLF11

This is a list of pathogenic ClinVar variants found in the KLF11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-10043421-A-G			Likely benign (Aug 25, 2018)
2-10043427-C-CGGCCGGGCACG			Benign (Aug 17, 2018)
2-10043500-G-A			Likely benign (Apr 02, 2021)
2-10043558-G-A		Maturity-onset diabetes of the young type 7	Uncertain significance (Apr 27, 2017)
2-10043560-C-T			Likely benign (Feb 28, 2021)
2-10043571-C-T		Maturity-onset diabetes of the young type 7	Uncertain significance (Jan 13, 2018)
2-10043609-G-A		Maturity-onset diabetes of the young type 7	Uncertain significance (Jan 12, 2018)
2-10043613-C-T		Maturity-onset diabetes of the young type 7	Uncertain significance (Jan 12, 2018)
2-10043621-TGCC-T		Maturity onset diabetes mellitus in young	Benign (Aug 10, 2019)
2-10043621-T-TGCC		Maturity onset diabetes mellitus in young	Conflicting classifications of pathogenicity (Jun 01, 2023)
2-10043634-G-A		Maturity-onset diabetes of the young type 7	Uncertain significance (Jan 12, 2018)
2-10043641-G-A		Maturity-onset diabetes of the young type 7	Uncertain significance (Jan 13, 2018)
2-10043686-G-A		Maturity-onset diabetes of the young type 7	Uncertain significance (May 05, 2022)
2-10043708-G-A		not specified	Likely benign (-)
2-10043728-G-A			Likely benign (Apr 02, 2021)
2-10043734-C-T		Maturity-onset diabetes of the young type 7	Uncertain significance (Jan 12, 2018)
2-10043736-C-T		not specified	Uncertain significance (Jun 02, 2023)
2-10043738-G-C		not specified	Uncertain significance (Aug 20, 2015)
2-10043739-G-A		Hyperglycemia;Maturity onset diabetes mellitus in young	Uncertain significance (Jan 01, 2017)
2-10043740-C-G		not specified	Likely benign (Sep 29, 2020)
2-10043741-C-T		Maturity-onset diabetes of the young type 7	Uncertain significance (Apr 27, 2017)
2-10043749-C-T		not specified	Likely benign (Oct 29, 2023)
2-10043751-C-A		KLF11-related disorder	Uncertain significance (Jan 19, 2024)
2-10043752-G-A			Likely benign (Jul 22, 2022)
2-10043758-A-G			Uncertain significance (Nov 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF11	protein_coding	protein_coding	ENST00000305883	4	11988

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.32e-9	0.160	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.50	362	290	1.25	0.0000170	3314
Missense in Polyphen		90	90.995	0.98907		988
Synonymous	-3.20	160	116	1.38	0.00000695	1090
Loss of Function	0.253	13	14.0	0.927	8.90e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000459	0.000271
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000381	0.000381
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000381	0.000381
South Asian	0.000294	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor (PubMed:9748269, PubMed:10207080). Activates the epsilon- and gamma-globin gene promoters and, to a much lower degree, the beta-globin gene and represses promoters containing SP1-like binding inhibiting cell growth (PubMed:9748269, PubMed:10207080, PubMed:16131492). Represses transcription of SMAD7 which enhances TGF-beta signaling (By similarity). Induces apoptosis (By similarity). {ECO:0000250|UniProtKB:Q8K1S5, ECO:0000269|PubMed:10207080, ECO:0000269|PubMed:16131492}.
• Disease: DISEASE: Maturity-onset diabetes of the young 7 (MODY7) [MIM:610508]: A form of diabetes that is characterized by an autosomal dominant mode of inheritance, onset in childhood or early adulthood (usually before 25 years of age), a primary defect in insulin secretion and frequent insulin-independence at the beginning of the disease. {ECO:0000269|PubMed:15774581}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: B Cell Receptor Signaling Pathway;TGF-beta Signaling Pathway;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.815
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.57

Haploinsufficiency Scores

• pHI: 0.108
• hipred: Y
• hipred_score: 0.539
• ghis: 0.480

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: Klf11
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of transcription involved in G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;apoptotic process;negative regulation of cell population proliferation;positive regulation of apoptotic process;cellular response to peptide
• Cellular component: nucleus;nucleoplasm;cytosol;focal adhesion;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;transcription regulatory region DNA binding;metal ion binding