KLHL14

Chr 18

kelch like family member 14

The encoded protein contains six Kelch domains and localizes to the endoplasmic reticulum where it interacts with torsin-1A. Biallelic mutations cause autosomal recessive intellectual disability with seizures and spasticity. This gene is highly constrained against loss-of-function variants (LOEUF 0.495), suggesting intolerance to protein loss.

Summary from RefSeq
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0
Active trials
3
Pubs (1 yr)
0
P/LP submissions
P/LP missense
0.49
LOEUF
Multiple*
Mechanism· predicted
Clinical SummaryKLHL14
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.49LOEUF
pLI 0.054
Z-score 3.63
OE 0.27 (0.160.49)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.60Z-score
OE missense 0.76 (0.690.84)
275 obs / 360.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.27 (0.160.49)
00.351.4
Missense OE0.76 (0.690.84)
00.61.4
Synonymous OE1.12
01.21.6
LoF obs/exp: 8 / 29.1Missense obs/exp: 275 / 360.7Syn Z: -1.22
DN
0.7033th %ile
GOF
0.6931th %ile
LOF
0.3357th %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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

KLHL14 · 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

No active trials found for this gene.

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Clinical Literature
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