KLF6

Chr 10

KLF transcription factor 6

Also known as: BCD1, CBA1, COPEB, CPBP, GBF, PAC1, ST12, ZF9

NCBI Gene: 1316ENSG00000067082UniProt: Q99612OMIM: 602053

KLF6 encodes a zinc finger transcription factor that activates gene transcription by binding GC box motifs and may function in B-cell growth and development. Mutations cause gastric cancer and prostate cancer as somatic (acquired) alterations rather than inherited germline conditions. This gene is highly constrained against loss-of-function variants (pLI 0.98, LOEUF 0.25), indicating it is essential for normal cellular function.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismLOEUF 0.252 OMIM phenotypes
Clinical Summary— KLF6
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
34 unique Pathogenic / Likely Pathogenic· 20 VUS of 77 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.25LOEUF
pLI 0.979
Z-score 3.19
OE 0.00 (0.00–0.25)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
1.85Z-score
OE missense 0.59 (0.50–0.70)
95 obs / 161.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–0.25)
0≤0.351.4
Missense OE0.59 (0.50–0.70)
0≤0.61.4
Synonymous OE1.08
0≤1.21.6
LoF obs/exp: 0 / 11.9Missense obs/exp: 95 / 161.2Syn Z: -0.54
DN
0.3196th %ile
GOF
0.2497th %ile
LOF
0.85top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.25

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic32
Likely Pathogenic2
VUS20
Likely Benign2
Benign3
32
Pathogenic
2
Likely Pathogenic
20
VUS
2
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
5
26
0
32
Likely Pathogenic
0
0
2
0
2
VUS
0
14
6
0
20
Likely Benign
1
0
0
1
2
Benign
0
1
0
2
3
Total22034359

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

KLF6 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Identification of genetic associations and functional SNPs of bovine KLF6 gene on milk production traits in Chinese holstein
Liu Y et al.·BMC Genom Data
2023Functional
Kruppel-Like Factor 6 Splice Variant 1: An Oncogenic Transcription Factor Involved in the Progression of Multiple Malignant Tumors
Hu K et al.·Front Cell Dev Biol
2021
Silencing KLF6 Alleviates Cigarette Smoke Extract-Induced Mitochondrial Dysfunction in Bronchial Epithelial Cells by SIRT4 Upregulation
Wan M et al.·Int J Chron Obstruct Pulmon Dis
2024
Ropinirole suppresses LPS-induced periodontal inflammation by inhibiting the NAT10 in an ac4C-dependent manner
Liao H et al.·BMC Oral Health
2024
Deciphering the Key Regulatory Roles of KLF6 and Bta-miR-148a on Milk Fat Metabolism in Bovine Mammary Epithelial Cells
Iqbal A et al.·Genes (Basel)
2022
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients