KLF13

Chr 15

KLF transcription factor 13

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

NCBI Gene: 51621 ENSG00000169926 OMIM: 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.

GeneReviews OMIM ResearchSummary from RefSeq, UniProt

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]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.93

Clinical Summary— KLF13

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Gene-Disease Validity (ClinGen)

congenital heart disease · ADModerate

Moderate evidence — consider for supplementary testing

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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

58 VUS of 75 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — KLF13

Authoritative clinical overview · Recommended first read

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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 OE?0.20 (0.07–0.93)

0≤0.351.4

Missense OE?0.46 (0.37–0.58)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 1 / 5.1Missense obs/exp: 52 / 112.1Syn Z: -0.46

This gene — mechanism propensity

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

75 submitted variants in ClinVar

ClinVar

Classification Summary

VUS58

Likely Benign10

Benign2

Conflicting1

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	0	58	0	0	58
Likely Benign	0	1	0	9	10
Benign	0	0	0	2	2
Conflicting	—				1
Total	0	59	0	11	71

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

View in ClinVar →

175 pathogenic / likely-pathogenic (of 230) ClinVar copy-number / structural variants overlap KLF13 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →