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

No genCC data.

ClinVar

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

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.

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				4	1	5
missense		1	22		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1			1
non coding					1	1
Total	0	1	23	4	3

Variants in KLF7

This is a list of pathogenic ClinVar variants found in the KLF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-207081229-A-G		Inborn genetic diseases	Uncertain significance (Mar 05, 2024)
2-207081268-G-A			Uncertain significance (May 25, 2022)
2-207088517-G-A			Benign (Mar 05, 2018)
2-207088525-C-T		intellectual deficiency • KLF7-related disorder • Neurodevelopmental disorder • Inborn genetic diseases	Pathogenic/Likely pathogenic (Jul 05, 2023)
2-207088530-C-T			Uncertain significance (Feb 07, 2024)
2-207123806-G-T			Uncertain significance (Feb 09, 2024)
2-207123885-C-A		Inborn genetic diseases	Uncertain significance (Mar 28, 2023)
2-207123887-C-A			Uncertain significance (Oct 12, 2022)
2-207123932-C-G		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
2-207123941-G-A		Inborn genetic diseases	Uncertain significance (Apr 09, 2024)
2-207124020-T-G			Uncertain significance (Sep 01, 2019)
2-207124052-G-A		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
2-207124056-T-C		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
2-207124070-C-T		Inborn genetic diseases	Uncertain significance (May 27, 2022)
2-207124071-G-C			Uncertain significance (Feb 14, 2024)
2-207124082-G-A			Uncertain significance (Apr 08, 2022)
2-207124083-G-T		Inborn genetic diseases	Uncertain significance (Mar 12, 2024)
2-207124088-G-A		KLF7-related neurodevelopmental disorder	Uncertain significance (Jan 29, 2024)
2-207124097-G-A		Inborn genetic diseases • KLF7-related neurodevelopmental disorder • Mild expressive language delay;Delayed gross motor development • Anxiety;Intellectual disability	Conflicting classifications of pathogenicity (Apr 04, 2024)
2-207124109-A-C		KLF7-related disorder	Uncertain significance (Oct 28, 2022)
2-207124114-G-A		KLF7-related disorder	Likely benign (Sep 05, 2019)
2-207124135-G-A		KLF7-related disorder	Likely benign (Jan 13, 2020)
2-207124179-G-A		Inborn genetic diseases	Uncertain significance (Jan 18, 2022)
2-207124205-C-T		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
2-207124220-T-G			Uncertain significance (Apr 15, 2022)

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
0.982	0.0182	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

Haploinsufficiency Scores

• pHI: 0.731
• hipred: Y
• hipred_score: 0.600
• ghis: 0.600

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

Mouse Genome Informatics

• Gene name: Klf7
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory 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); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton 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); cellular phenotype; homeostasis/metabolism phenotype

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