KLF13

Chr 15

KLF transcription factor 13

Also known as: BTEB3, FKLF2, NSLP1, RFLAT-1, RFLAT1

NCBI Gene: 51621ENSG00000169926UniProt: Q9Y2Y9

KLF13 belongs to a family of transcription factors that contain 3 classical zinc finger DNA-binding domains consisting of a zinc atom tetrahedrally coordinated by 2 cysteines and 2 histidines (C2H2 motif). These transcription factors bind to GC-rich sequences and related GT and CACCC boxes (Scohy et al., 2000 [PubMed 11087666]).[supplied by OMIM, Mar 2008]

295
ClinVar variants
172
Pathogenic / LP
0.40
pLI score
0
Active trials
Clinical Summary— KLF13
🧬
Gene-Disease Validity (ClinGen)
congenital heart disease · ADModerate

Moderate evidence — consider for supplementary testing

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.20) despite low pLI — interpret in context.
📋
ClinVar Variants
172 Pathogenic / Likely Pathogenic· 105 VUS of 295 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.
0.93LOEUF
pLI 0.404
Z-score 1.68
OE 0.20 (0.07–0.93)
Tolerant

Typical tolerance to LoF variation

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.
2.02Z-score
OE missense 0.46 (0.37–0.58)
52 obs / 112.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

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.0.20 (0.07–0.93)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.46 (0.37–0.58)
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.1.08
0≤1.21.6
LoF obs/exp: 1 / 5.1Missense obs/exp: 52 / 112.1Syn Z: -0.46

ClinVar Variant Classifications

295 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic165
Likely Pathogenic7
VUS105
Likely Benign9
Benign3
Conflicting6
165
Pathogenic
7
Likely Pathogenic
105
VUS
9
Likely Benign
3
Benign
6
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
165
0
165
Likely Pathogenic
0
0
7
0
7
VUS
0
58
47
0
105
Likely Benign
0
1
0
8
9
Benign
0
0
0
3
3
Conflicting
—6
Total05921911295

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

View in ClinVar →

Protein Context — Lollipop Plot

KLF13 · 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
📖
GeneReview available — KLF13
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Bioinformatic Evaluation of KLF13 Genetic Variant: Implications for Neurodevelopmental and Psychiatric Symptoms.
Vinci M et al.·Genes (Basel)
2024
KLF13 promotes breast cancer progression through the HTRA1 and the Hedgehog signaling pathway.
Huang M et al.·Breast Cancer
2025
Kruppel-like factor 13 acts as a tumor suppressor in thyroid carcinoma by downregulating IFIT1.
Liu Y et al.·Biol Direct
2023
Identification and analysis of KLF13 variants in patients with congenital heart disease.
Li W et al.·BMC Med Genet
2020Cohort
Integrative miRNA-mRNA profiling uncovers mechanisms of belimumab action in systemic lupus erythematosus.
Royo M et al.·Front Immunol
2025Functional
A new KLF13 loss-of-function mutation responsible for sporadic dilated cardiomyopathy.
Tang X et al.·Mol Biol Rep
2025
Early-life environmental exposures interact with genetic susceptibility variants in pediatric patients with eosinophilic esophagitis.
Jensen ET et al.·J Allergy Clin Immunol
2018Cohort
TET3-mediated novel regulatory mechanism affecting trophoblast invasion and migration: Implications for preeclampsia development.
Wang C et al.·Placenta
2024Functional
[Research progress on the roles of Krüppel-like factors in muscle tissues].
Zhuang ZH et al.·Yi Chuan
2018Review
Genetic counseling of prenatally detected familial 15q13.2q13.3 microdeletion encompassing CHRNA7 and OTUD7A with asymptomatic carriers in the family.
Chen CP et al.·Taiwan J Obstet Gynecol
2025Case report
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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