KLF6

KLF transcription factor 6, the group of Kruppel like factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 10:3775996-3785281

Previous symbols: [ "BCD1", "ST12", "COPEB" ]

Links

ENSG00000067082 ∙ NCBI:1316 ∙ OMIM:602053 ∙ HGNC:2235 ∙ Uniprot:Q99612 ∙ 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 KLF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLF6 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	2	3
missense			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	3

Variants in KLF6

This is a list of pathogenic ClinVar variants found in the KLF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-3779477-C-T		Hypotension	not provided (-)
10-3779493-T-A		Hypotension	not provided (-)
10-3780072-C-T		Hypotension	not provided (-)
10-3780085-G-A		Hypotension	not provided (-)
10-3780231-T-C			not provided (-)
10-3781535-C-T		not specified	not provided (Sep 19, 2013)
10-3781580-G-A		not specified	not provided (Sep 19, 2013)
10-3781613-G-A		not specified	not provided (Sep 19, 2013)
10-3781714-C-T		Hypotension	Benign/Likely benign (Dec 01, 2022)
10-3781723-C-T			Benign (Jun 19, 2017)
10-3781811-A-G		Prostate cancer, somatic	Pathogenic (Dec 21, 2001)
10-3781821-G-A		Hypotension	not provided (-)
10-3781824-C-T		not specified	Benign (May 17, 2018)
10-3781852-G-T		Gastric cancer	Pathogenic (Jun 30, 2005)
10-3781883-G-A		not specified	Uncertain significance (Oct 17, 2023)
10-3781889-G-A		not specified	not provided (Sep 19, 2013)
10-3781892-G-T		not specified	Uncertain significance (Mar 18, 2024)
10-3781907-G-T		Prostate cancer, somatic	Pathogenic (Dec 21, 2001)
10-3781949-G-T		Prostate cancer, somatic	Pathogenic (Dec 21, 2001)
10-3781971-A-G		Prostate cancer, somatic	Pathogenic (Dec 21, 2001)
10-3782041-G-T		not specified	not provided (Sep 19, 2013)
10-3782086-G-A			Benign (May 17, 2018)
10-3782127-A-G		Prostate cancer, somatic	Pathogenic (Dec 21, 2001)
10-3782215-C-G			not provided (-)
10-3784938-G-T		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLF6	protein_coding	protein_coding	ENST00000497571	4	9286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0205	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	95	161	0.589	0.00000957	1857
Missense in Polyphen		46	84.584	0.54384		973
Synonymous	-0.538	76	70.3	1.08	0.00000485	542
Loss of Function	3.19	0	11.9	0.00	6.01e-7	141

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)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator (By similarity). Binds a GC box motif. Could play a role in B-cell growth and development. {ECO:0000250}.
• Disease: DISEASE: Gastric cancer (GASC) [MIM:613659]: A malignant disease which starts in the stomach, can spread to the esophagus or the small intestine, and can extend through the stomach wall to nearby lymph nodes and organs. It also can metastasize to other parts of the body. The term gastric cancer or gastric carcinoma refers to adenocarcinoma of the stomach that accounts for most of all gastric malignant tumors. Two main histologic types are recognized, diffuse type and intestinal type carcinomas. Diffuse tumors are poorly differentiated infiltrating lesions, resulting in thickening of the stomach. In contrast, intestinal tumors are usually exophytic, often ulcerating, and associated with intestinal metaplasia of the stomach, most often observed in sporadic disease. {ECO:0000269|PubMed:15824733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Prostate cancer (PC) [MIM:176807]: A malignancy originating in tissues of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269|PubMed:11752579}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Adipogenesis;Aryl Hydrocarbon Receptor;TGF-beta Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.321

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.799
• hipred: Y
• hipred_score: 0.794
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klf6
• Phenotype: growth/size/body region 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); endocrine/exocrine gland phenotype; cellular 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); reproductive system phenotype; embryo phenotype; liver/biliary system phenotype

Zebrafish Information Network

• Gene name: klf6a
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cytokine-mediated signaling pathway;B cell differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: fibrillar center;nucleus;nucleolus;cytosol;intracellular membrane-bounded organelle
• 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;double-stranded DNA binding;protein binding;metal ion binding