GeneBe

KLF6

protein-coding

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

Gene summary

This gene encodes a member of the Kruppel-like family of transcription factors. The zinc finger protein is a transcriptional activator, and functions as a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene, some of which are implicated in carcinogenesis. [provided by RefSeq, May 2009]

Previous symbols:
  • BCD1
  • ST12
  • COPEB

MANE transcript

NM_001300.6

Inheritance

—

ClinVar variants

P:6U:22B:5

Top phenotype

Prostate cancer, somatic

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr10:3,775,996-3,785,281

External References & Databases

Ensembl (ENSG00000067082)NCBI Gene (1316)OMIM (602053)HGNC:2235GenCCUniProt (Q99612)AlphaFoldClinVar (KLF6)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~9.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KLF6 variants in ClinVar

5 Conditions Cataloged
not specifiedTotal: 21
not providedTotal: 5
Prostate cancer, somaticTotal: 5
HypotensionTotal: 4
Gastric cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001300.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
clinvar
 4
missense
5
clinvar
20
clinvar
1
clinvar
 26
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total60222333

Highest pathogenic variant AF is 6.84105e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001300.6RefSeqNP_001291.34MANE Select
ENST00000497571.6EnsemblENSP00000419923.14MANE Select
NM_001160124.2RefSeqNP_001153596.14Standard
NM_001160125.2RefSeqNP_001153597.13Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
klf6aDanio rerio

Structure: nucleate erythrocyte

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Adipogenesis
  • Aryl Hydrocarbon Receptor
  • TGF-beta Signaling Pathway

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

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

Cellular Component

  • fibrillar center
  • nucleus
  • nucleolus
  • cytosol
  • intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000497571
Coding exons
4
Length
9286
Individuals with no LoFs
125746
Homozygous LoFs
0
Heterozygous LoFs
2
Defined
125748
p
0.00000795
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.85951610.5890.000009571857
Missense (PolyPhen)4684.5840.54384973
Synonymous-0.5387670.31.080.00000485542
Loss of Function3.19011.90.006.01e-7141

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.321

Intolerance Scores

RVIS EVS
-0.07
RVIS percentile EVS
48.12

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.891

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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