KLF13

Chr 15

KLF transcription factor 13

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

NCBI Gene: 51621ENSG00000169926UniProt: Q9Y2Y9OMIM: 605328

KLF13 encodes a zinc finger transcription factor that binds to GC-rich DNA sequences to regulate gene expression, including activation of genes in erythroid cells and repression through interaction with corepressor complexes. Mutations cause an autosomal dominant neurodevelopmental disorder with intellectual disability, developmental delay, and variable features including seizures and behavioral abnormalities. The gene has moderate tolerance to loss-of-function variants based on population genetics data.

GeneReviewsOMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.93
Clinical Summary— KLF13
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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.
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ClinVar Variants
174 unique Pathogenic / Likely Pathogenic· 105 VUS of 303 total submissions
Explore recent and relevant literature in Research Assistant →
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GeneReview available — KLF13
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.93LOEUF
pLI 0.404
Z-score 1.68
OE 0.20 (0.07–0.93)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
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
LoF OE0.20 (0.07–0.93)
0≤0.351.4
Missense OE0.46 (0.37–0.58)
0≤0.61.4
Synonymous OE1.08
0≤1.21.6
LoF obs/exp: 1 / 5.1Missense obs/exp: 52 / 112.1Syn Z: -0.46
DN
0.5378th %ile
GOF
0.4381th %ile
LOF
0.65top 25%

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

LOFprediction above median

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

303 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic167
Likely Pathogenic7
VUS105
Likely Benign10
Benign2
Conflicting7
167
Pathogenic
7
Likely Pathogenic
105
VUS
10
Likely Benign
2
Benign
7
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
167
0
167
Likely Pathogenic
0
0
7
0
7
VUS
0
58
47
0
105
Likely Benign
0
1
0
9
10
Benign
0
0
0
2
2
Conflicting
—7
Total05922111298

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.

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
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