KLF17

Chr 1

KLF transcription factor 17

Also known as: ZLF393, ZNF393, Zfp393

NCBI Gene: 128209ENSG00000171872UniProt: Q5JT82

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within gamete generation. Predicted to be located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

87
ClinVar variants
9
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— KLF17
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
9 Pathogenic / Likely Pathogenic· 68 VUS of 87 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.36LOEUF
pLI 0.000
Z-score 0.49
OE 0.87 (0.57–1.36)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.12Z-score
OE missense 1.02 (0.92–1.14)
239 obs / 233.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.87 (0.57–1.36)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.02 (0.92–1.14)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.05
0≤1.21.6
LoF obs/exp: 14 / 16.1Missense obs/exp: 239 / 233.6Syn Z: -0.37

ClinVar Variant Classifications

87 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic8
Likely Pathogenic1
VUS68
Likely Benign10
8
Pathogenic
1
Likely Pathogenic
68
VUS
10
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
8
0
8
Likely Pathogenic
0
0
1
0
1
VUS
0
62
6
0
68
Likely Benign
0
10
0
0
10
Benign
0
0
0
0
0
Total07215087

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

View in ClinVar →

Protein Context — Lollipop Plot

KLF17 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Novel FUS-KLF17 and EWSR1-KLF17 fusions in myoepithelial tumors.
Huang SC et al.·Genes Chromosomes Cancer
2015
KLF17 Expression in Colorectal Carcinoma and Its Clinical Significance.
Gao HL et al.·Zhongguo Yi Xue Ke Xue Yuan Xue Bao
2016
Clinical significance and biological role of KLF17 as a tumour suppressor in colorectal cancer.
Jiang X et al.·Oncol Rep
2019
Prognostic value of KLFs family genes in renal clear cell carcinoma.
Fu M et al.·Sci Rep
2024
Low expression of KLF17 is associated with tumor invasion in esophageal carcinoma.
Li S et al.·Int J Clin Exp Pathol
2015
Down-regulated KLF17 expression is associated with tumor invasion and poor prognosis in hepatocellular carcinoma.
Liu FY et al.·Med Oncol
2013
Myoepithelial tumors of soft tissue and bone in children and young adults: A clinicopathologic study of 40 cases occurring in patients ≤ 21 Years of age.
Logan SJ et al.·Hum Pathol
2024Cohort
Suppressed Krüppel‑like factor 17 expression induces tumor proliferation, metastasis and a poor prognosis in papillary thyroid carcinoma.
Ye WC et al.·Mol Med Rep
2014
Up-regulation of KLF17 expression increases the sensitivity of gastric cancer to 5-fluorouracil.
An ZJ et al.·Int J Immunopathol Pharmacol
2021
Reduced expression of Krüppel-like factor 17 is related to tumor growth and poor prognosis in lung adenocarcinoma.
Cai XD et al.·Biochem Biophys Res Commun
2012
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Novel EPS15::KLF17 and EPS15L1::KLF17 Fusions Define a Distinctive Group of MUC4-Positive Spindled to Epithelioid Sarcomas.
Malik F et al.·Am J Surg Pathol
2026
Pseudoglandular Schwannoma With FUS::KLF17 Fusion: Broadening the Spectrum of FUS-Associated Tumors.
Givi J et al.·Genes Chromosomes Cancer
2025🔓 Open Access
Maternal KLF17 controls zygotic genome activation by acting as a messenger for RNA Pol II recruitment in mouse embryos.
Hu Y et al.·Dev Cell
2024Functional
KLF17 is an important regulatory component of the transcriptomic response of Atlantic salmon macrophages to Piscirickettsia salmonis infection.
Pérez-Stuardo D et al.·Front Immunol
2023🔓 Open Access
Anti-oncogenic mechanism of KLF17 in colon cancer by repressing cell migration and invasion via FHL1 upregulation.
Yi S et al.·Chin J Physiol
2023Functional
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools