KLF10

KLF transcription factor 10, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 8:102648784-102655725

Previous symbols: [ "TIEG" ]

Links

ENSG00000155090 ∙ NCBI:7071 ∙ OMIM:601878 ∙ HGNC:11810 ∙ Uniprot:Q13118 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypertrophic cardiomyopathy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLF10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF10 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	59	4	64
missense			101	2	4	107
nonsense						0
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			1	3		4
non coding				12	15	27
Total	0	0	106	73	23

Variants in KLF10

This is a list of pathogenic ClinVar variants found in the KLF10 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-102649965-G-A			Benign (May 21, 2021)
8-102649991-G-A			Benign (Sep 04, 2018)
8-102650125-C-T			Likely benign (Sep 08, 2022)
8-102650147-A-G			Likely benign (Mar 26, 2021)
8-102650150-G-A			Likely benign (Oct 20, 2023)
8-102650152-T-C		not specified	Uncertain significance (May 14, 2024)
8-102650154-G-A		not specified	Uncertain significance (Sep 27, 2022)
8-102650163-G-A			Uncertain significance (Sep 25, 2021)
8-102650165-A-C			Uncertain significance (Jul 31, 2021)
8-102650176-G-A			Likely benign (Dec 21, 2021)
8-102650207-C-G			Uncertain significance (Aug 01, 2022)
8-102650219-T-C			Likely benign (Dec 03, 2023)
8-102650226-C-T			Uncertain significance (Aug 24, 2022)
8-102650227-G-A		not specified	Uncertain significance (Nov 08, 2024)
8-102650232-G-C			Uncertain significance (May 12, 2021)
8-102650265-C-T			Uncertain significance (Oct 05, 2021)
8-102650270-G-A			Likely benign (Jan 29, 2023)
8-102650279-G-A			Likely benign (Apr 27, 2023)
8-102650285-C-T			Likely benign (Feb 20, 2022)
8-102650287-C-T			Uncertain significance (Oct 24, 2022)
8-102650303-C-T			Likely benign (Nov 08, 2023)
8-102650318-G-A			Likely benign (Jul 07, 2023)
8-102650354-T-C			Likely benign (Jan 13, 2024)
8-102650355-T-C			Uncertain significance (Aug 30, 2023)
8-102650376-C-T			Uncertain significance (Nov 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF10	protein_coding	protein_coding	ENST00000285407	4	7124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00458	0.968	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	204	268	0.761	0.0000138	3144
Missense in Polyphen		27	78.134	0.34556		895
Synonymous	-1.42	117	99.1	1.18	0.00000528	977
Loss of Function	1.93	6	13.7	0.438	6.62e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor which binds to the consensus sequence 5'-GGTGTG-3'. Plays a role in the regulation of the circadian clock; binds to the GC box sequence in the promoter of the core clock component ARTNL/BMAL1 and represses its transcriptional activity. Regulates the circadian expression of genes involved in lipogenesis, gluconeogenesis, and glycolysis in the liver. Represses the expression of PCK2, a rate-limiting step enzyme of gluconeogenesis (By similarity). May play a role in the cell cycle regulation. {ECO:0000250|UniProtKB:O89091, ECO:0000269|PubMed:8584037}.
• Pathway: TGF-beta Signaling Pathway;TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.446
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.624
• hipred: Y
• hipred_score: 0.692
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf10
• Phenotype: cellular phenotype; homeostasis/metabolism 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); skeleton phenotype; limbs/digits/tail phenotype; neoplasm

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;skeletal system development;regulation of transcription by RNA polymerase II;transforming growth factor beta receptor signaling pathway;cell-cell signaling;circadian rhythm;cell population proliferation;negative regulation of cell population proliferation;cellular response to starvation;bone mineralization;somatic stem cell population maintenance;regulation of circadian rhythm;positive regulation of osteoclast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;cellular response to peptide
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;core promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;metal ion binding