KLF7

KLF transcription factor 7, the group of Kruppel like factors|Zinc fingers C2H2-type|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:207074137-207173856

Links

ENSG00000118263 ∙ NCBI:8609 ∙ OMIM:604865 ∙ HGNC:6350 ∙ Uniprot:O75840 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Definitive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLF7 gene.

• Inborn_genetic_diseases (37 variants)
• not_provided (27 variants)
• KLF7-related_disorder (7 variants)
• KLF7-related_neurodevelopmental_disorder (3 variants)
• Neurodevelopmental_disorder (2 variants)
• not_specified (2 variants)
• Mild_expressive_language_delay (1 variants)
• Delayed_gross_motor_development (1 variants)
• intellectual_deficiency (1 variants)
• Anxiety (1 variants)
• Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003709.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	3	6
missense		2	53	8		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	2	53	11	3

Highest pathogenic variant AF is 0.0000020521409

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF7	protein_coding	protein_coding	ENST00000309446	4	93131

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	101	190	0.530	0.0000120	1960
Missense in Polyphen		12	66.12	0.18149		688
Synonymous	-1.01	95	83.2	1.14	0.00000597	609
Loss of Function	3.24	0	12.2	0.00	6.15e-7	146

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: dbNSFP

• Function: FUNCTION: Transcriptional activator. Binds in vitro to the CACCC motif of the beta-globin promoter and to the SP1 recognition sequence.
• Pathway: Adipogenesis (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.210
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.904

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;axon guidance;regulation of epidermal cell differentiation;positive regulation of transcription by RNA polymerase II;dendrite morphogenesis;regulation of insulin secretion;negative regulation of adipose tissue development
• Cellular component: nucleus
• 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;DNA-binding transcription factor activity;transcription coactivator activity;zinc ion binding