KLF15

KLF transcription factor 15, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 3:126342635-126357408

Links

ENSG00000163884 ∙ NCBI:28999 ∙ OMIM:606465 ∙ HGNC:14536 ∙ Uniprot:Q9UIH9 ∙ 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 KLF15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF15 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	1	0

Variants in KLF15

This is a list of pathogenic ClinVar variants found in the KLF15 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-126343740-C-A		not specified	Uncertain significance (Feb 28, 2024)
3-126343741-G-T		not specified	Uncertain significance (Jun 30, 2022)
3-126343750-G-A		not specified	Uncertain significance (May 26, 2022)
3-126343784-C-A		not specified	Uncertain significance (May 26, 2022)
3-126343791-A-C		not specified	Uncertain significance (Jun 13, 2024)
3-126351869-C-T		not specified	Uncertain significance (Oct 12, 2022)
3-126351893-G-A		not specified	Uncertain significance (Nov 22, 2022)
3-126351958-T-C		not specified	Uncertain significance (Jan 24, 2023)
3-126351971-T-C		not specified	Uncertain significance (Mar 24, 2023)
3-126351999-C-A		not specified	Uncertain significance (Feb 14, 2023)
3-126352009-A-G		not specified	Uncertain significance (Mar 29, 2022)
3-126352136-C-T		not specified	Uncertain significance (Mar 21, 2022)
3-126352198-G-T		not specified	Uncertain significance (Dec 12, 2023)
3-126352199-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-126352211-A-G		not specified	Uncertain significance (Jun 03, 2022)
3-126352256-T-A		not specified	Uncertain significance (Jan 04, 2024)
3-126352265-A-C		not specified	Uncertain significance (Sep 20, 2022)
3-126352277-G-A		not specified	Uncertain significance (Jan 17, 2023)
3-126352333-C-G		not specified	Uncertain significance (Apr 10, 2023)
3-126352351-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-126352352-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-126352520-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-126352526-C-T		not specified	Uncertain significance (Mar 20, 2024)
3-126352553-C-T		not specified	Uncertain significance (Dec 14, 2023)
3-126352732-T-C		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF15	protein_coding	protein_coding	ENST00000296233	2	14808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.488	0.507	125536	0	5	125541	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.985	202	245	0.823	0.0000157	2666
Missense in Polyphen		51	86.406	0.59024		973
Synonymous	0.151	104	106	0.981	0.00000735	884
Loss of Function	2.39	2	10.3	0.195	5.14e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.0000995
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000380	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that binds to the GA element of the CLCNKA promoter. Binds to the KCNIP2 promoter and regulates KCNIP2 circadian expression in the heart (By similarity). Is a repressor of CTGF expression, involved in the control of cardiac fibrosis. It is also involved in the control of cardiac hypertrophy acting through the inhibition of MEF2A and GATA4 (By similarity). Involved in podocyte differentiation (By similarity). Inhibits MYOCD activity. Is a negative regulator of TP53 acetylation. Inhibits NF-kappa-B activation through repression of EP300-dependent RELA acetylation. {ECO:0000250, ECO:0000269|PubMed:18586263, ECO:0000269|PubMed:20375365, ECO:0000269|PubMed:20566642, ECO:0000269|PubMed:23999430}.
• Disease: DISEASE: Note=KLF15 deficiency results in loss of rhythmic QT variation and abnormal heart repolarization (PubMed:22367544). It may play a role in susceptibility to ventricular arrhythmias (PubMed:22367544), and development of pathological cardiac hypertrophy leading to heart failure (PubMed:20375365). {ECO:0000269|PubMed:20375365, ECO:0000269|PubMed:22367544}.
• Pathway: White fat cell differentiation;Adipogenesis;BMAL1-CLOCK,NPAS2 activates circadian gene expression;White fat cell differentiation;Transcriptional cascade regulating adipogenesis;Circadian Clock;BMAL1:CLOCK,NPAS2 activates circadian gene expression (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.200
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.382
• hipred: Y
• hipred_score: 0.559
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf15
• Phenotype: liver/biliary system 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; 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); immune system phenotype; renal/urinary system phenotype; 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); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cellular glucose homeostasis;regulation of transcription by RNA polymerase II;glial cell differentiation;cardiac muscle hypertrophy in response to stress;response to insulin;positive regulation of transcription by RNA polymerase II;positive regulation of glucose import;glomerular visceral epithelial cell differentiation;negative regulation of peptidyl-lysine acetylation
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;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 regulatory region DNA binding;metal ion binding