KLF2

KLF transcription factor 2, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 19:16324826-16328685

Links

ENSG00000127528 ∙ NCBI:10365 ∙ OMIM:602016 ∙ HGNC:6347 ∙ Uniprot:Q9Y5W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pulmonary arterial hypertension (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF2 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				1		1
missense			26		2	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	26	1	4

Variants in KLF2

This is a list of pathogenic ClinVar variants found in the KLF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-16324960-A-G		not specified	Uncertain significance (May 18, 2023)
19-16324988-G-C		not specified	Uncertain significance (Oct 05, 2021)
19-16325042-C-T			Benign (May 13, 2021)
19-16325292-T-C		not specified	Uncertain significance (Sep 13, 2023)
19-16325307-T-C		not specified	Uncertain significance (Nov 07, 2022)
19-16325366-C-G		not specified	Uncertain significance (Jul 09, 2021)
19-16325403-C-G		not specified	Uncertain significance (Dec 10, 2024)
19-16325414-G-A		not specified	Uncertain significance (Dec 14, 2022)
19-16325450-C-G		not specified	Uncertain significance (Jun 30, 2024)
19-16325451-T-C			Benign (May 04, 2021)
19-16325454-G-C		not specified	Uncertain significance (Nov 19, 2024)
19-16325456-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-16325501-G-A		not specified	Uncertain significance (Feb 24, 2022)
19-16325531-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-16325537-G-C		not specified	Uncertain significance (Dec 15, 2023)
19-16325565-G-A			Benign (Dec 17, 2018)
19-16325570-C-T		not specified	Uncertain significance (Oct 27, 2021)
19-16325576-G-A		not specified	Uncertain significance (Oct 22, 2021)
19-16325588-G-A		not specified	Uncertain significance (Oct 04, 2022)
19-16325590-G-T		not specified	Uncertain significance (Sep 29, 2023)
19-16325655-A-C		not specified	Uncertain significance (Nov 30, 2021)
19-16325675-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-16325702-G-T		not specified	Uncertain significance (Sep 29, 2023)
19-16325714-T-G		not specified	Uncertain significance (Oct 25, 2024)
19-16325738-C-T		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF2	protein_coding	protein_coding	ENST00000248071	3	3058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.560	0.428	125011	0	1	125012	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	47	113	0.415	0.00000628	2147
Missense in Polyphen		3	14.781	0.20296		278
Synonymous	-0.486	53	48.7	1.09	0.00000275	782
Loss of Function	2.04	1	6.68	0.150	3.38e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds to the CACCC box in the promoter of target genes such as HBB/beta globin or NOV and activates their transcription. {ECO:0000269|PubMed:21063504}.
• Pathway: FoxO signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);White fat cell differentiation;EV release from cardiac cells and their functional effects;White fat cell differentiation;Transcriptional cascade regulating adipogenesis (Consensus)

Haploinsufficiency Scores

• pHI: 0.0971
• hipred: Y
• hipred_score: 0.751

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.704

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf2
• Phenotype: craniofacial phenotype; muscle phenotype; homeostasis/metabolism 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; 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; growth/size/body region phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: klf2b
• Affected structure: margin
• Phenotype tag: abnormal
• Phenotype quality: differentiated

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cell morphogenesis;in utero embryonic development;regulation of transcription by RNA polymerase II;negative regulation of interleukin-6 production;multicellular organism growth;positive regulation of transcription from RNA polymerase II promoter in response to stress;regulation of gene expression, epigenetic;erythrocyte maturation;positive regulation of nitric oxide biosynthetic process;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of protein metabolic process;type I pneumocyte differentiation;cellular response to hydrogen peroxide;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to cycloheximide;cellular response to fluid shear stress;cellular response to laminar fluid shear stress;cellular stress response to acid chemical;cellular response to peptide;negative regulation of sprouting angiogenesis
• Cellular component: nuclear chromatin;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding