KLF18

Chr 1

KLF transcription factor 18

NCBI Gene: 105378952 ENSG00000283039 UniProt: A0A0U1RQI7 OMIM: 621009

KLF18 encodes a transcription factor that binds to specific DNA sequences to regulate gene expression by RNA polymerase II. Currently, no established human diseases have been definitively linked to mutations in this gene. The clinical significance of KLF18 variants in pediatric neurological conditions remains to be determined.

OMIM ResearchSummary from RefSeq

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Multiplemechanism

Clinical Summary— KLF18

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ClinVar Variants

10 total variants — no pathogenic classifications of 10 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

gnomad: Error: Gene not found

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

This gene — mechanism propensity

0.7229th %ile

GOF

0.7028th %ile

LOF

0.4331th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

10 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Benign10

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	0	0	0
Likely Benign	1	9	10
Benign	0	0	0
Total	1	9	10

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

View in ClinVar →

3 pathogenic / likely-pathogenic (of 4) ClinVar copy-number / structural variants overlap KLF18 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →