KLF5

KLF transcription factor 5, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 13:73054976-73077541

Previous symbols: [ "BTEB2" ]

Links

ENSG00000102554 ∙ NCBI:688 ∙ OMIM:602903 ∙ HGNC:6349 ∙ Uniprot:Q13887 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF5 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			26		1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	1

Variants in KLF5

This is a list of pathogenic ClinVar variants found in the KLF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-73059350-T-G		not specified	Uncertain significance (Mar 28, 2024)
13-73059353-G-A		not specified	Uncertain significance (Mar 24, 2023)
13-73059382-C-T		not specified	Uncertain significance (Nov 17, 2022)
13-73059401-C-T		not specified	Uncertain significance (Oct 30, 2024)
13-73059448-C-G		not specified	Uncertain significance (Jul 09, 2021)
13-73059448-C-T		not specified	Uncertain significance (Oct 06, 2021)
13-73059465-C-G		not specified	Uncertain significance (Oct 27, 2023)
13-73059476-A-G		not specified	Uncertain significance (Nov 24, 2024)
13-73059493-C-T		not specified	Uncertain significance (Feb 13, 2024)
13-73059535-C-T		not specified	Uncertain significance (Dec 27, 2023)
13-73059536-C-T		not specified	Uncertain significance (Dec 14, 2023)
13-73059545-C-T		not specified	Uncertain significance (Mar 06, 2023)
13-73059556-G-T		not specified	Uncertain significance (Apr 04, 2024)
13-73059569-C-T		not specified	Uncertain significance (Jul 16, 2024)
13-73059587-A-C		not specified	Uncertain significance (Oct 16, 2023)
13-73061879-A-C		not specified	Uncertain significance (Mar 02, 2023)
13-73061912-A-G		not specified	Uncertain significance (Jan 26, 2022)
13-73061963-C-A		not specified	Uncertain significance (Aug 10, 2021)
13-73061964-A-C		not specified	Uncertain significance (Aug 10, 2021)
13-73061976-A-G		not specified	Uncertain significance (Feb 21, 2024)
13-73062026-A-G		not specified	Uncertain significance (Jun 20, 2024)
13-73062152-G-T		not specified	Uncertain significance (Sep 01, 2021)
13-73062213-A-C		not specified	Uncertain significance (Sep 27, 2022)
13-73062213-A-G		not specified	Uncertain significance (Oct 03, 2023)
13-73062254-C-G		not specified	Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF5	protein_coding	protein_coding	ENST00000377687	4	22563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.818	0.182	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	151	216	0.698	0.0000119	2967
Missense in Polyphen		56	101.23	0.55317		1204
Synonymous	0.192	84	86.3	0.974	0.00000531	933
Loss of Function	3.03	2	14.4	0.139	7.67e-7	178

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds to GC box promoter elements. Activates the transcription of these genes.
• Pathway: Transcriptional regulation of white adipocyte differentiation;White fat cell differentiation;Adipogenesis;Mesodermal Commitment Pathway;White fat cell differentiation;Transcriptional cascade regulating adipogenesis (Consensus)

Recessive Scores

• pRec: 0.223

Intolerance Scores

• loftool: 0.101
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.768
• hipred: Y
• hipred_score: 0.794
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Klf5
• Phenotype: vision/eye phenotype; digestive/alimentary phenotype; immune system phenotype; respiratory system phenotype; embryo phenotype; reproductive system 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); normal 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); 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); growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: klf5a
• Affected structure: gut
• Phenotype tag: abnormal
• Phenotype quality: immature

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;angiogenesis;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;positive regulation of cell population proliferation;microvillus assembly;regulation of microvillus assembly;skeletal muscle cell differentiation;positive regulation of fat cell differentiation;positive regulation of transcription by RNA polymerase II;intestinal epithelial cell development;cellular response to organic cyclic compound;cell-cell signaling via exosome;cellular response to peptide;positive regulation of pri-miRNA transcription by RNA polymerase II;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;nucleoplasm;Golgi apparatus;intracellular membrane-bounded organelle
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;transcription factor binding;metal ion binding