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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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KLHL15
kelch like family member 15
Chromosome X Β· Xp22.11
NCBI Gene: 80311Ensembl: ENSG00000174010.11HGNC: HGNC:29347UniProt: Q96M94
39PubMed Papers
21Diseases
0Drugs
3Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of double-strand break repair via homologous recombinationprotein bindingubiquitin-like ligase-substrate adaptor activityubiquitin-dependent protein catabolic processX-linked non-syndromic intellectual disabilityAbnormal brain morphologyIntellectual disabilityosteoarthritis, knee
✦AI Summary

KLHL15 encodes a substrate-specific adapter protein that functions within CUL3-based E3 ubiquitin ligase complexes to regulate protein degradation 1. The protein contains an N-terminal BTB/POZ domain and C-terminal kelch motifs, which are conserved across vertebrate species 2. KLHL15 targets multiple substrates for ubiquitination and proteasomal degradation through recognition of specific sequence motifs. Key substrates include the DNA repair protein CtIP/RBBP8, which contains a conserved FRY tripeptide motif essential for KLHL15 binding 1. By degrading CtIP, KLHL15 inhibits DNA-end resection and promotes error-prone non-homologous end joining over homologous recombination repair 1. KLHL15 also targets doublecortin (DCX) family proteins through similar FRY motifs, regulating neuronal dendrite development 3. Additionally, it promotes degradation of the PP2A regulatory subunit PPP2R5B/B'Ξ², facilitating exchange with other regulatory subunits and controlling phosphatase activity 4. Disease relevance includes X-linked intellectual disability, with pathogenic variants identified in affected families 56. The protein shows ubiquitous tissue expression and plays critical roles in DNA damage response, neuronal development, and cellular signaling through its regulation of protein stability 23.

Sources cited
1
KLHL15 functions as substrate adapter for CUL3 E3 ligase and targets CtIP for degradation via FRY motif recognition
PMID: 27561354
2
KLHL15 contains BTB/POZ domain and kelch motifs, shows ubiquitous expression
PMID: 15870933
3
KLHL15 targets doublecortin family proteins for degradation and regulates neuronal dendrite development
PMID: 33199366
4
KLHL15 promotes degradation of PP2A regulatory subunit B'Ξ²
PMID: 23135275
5
KLHL15 mutations cause X-linked intellectual disability
PMID: 25644381
6
KLHL15 variants identified in Chinese XLID families
PMID: 38684296
Disease Associationsβ“˜21
X-linked non-syndromic intellectual disabilityOpen Targets
0.47Moderate
Abnormal brain morphologyOpen Targets
0.27Weak
Intellectual disabilityOpen Targets
0.19Weak
osteoarthritis, kneeOpen Targets
0.16Weak
osteoarthritisOpen Targets
0.07Suggestive
benign prostatic hyperplasiaOpen Targets
0.02Suggestive
male reproductive organ cancerOpen Targets
0.02Suggestive
cancerOpen Targets
0.01Suggestive
X-linked intellectual disabilityOpen Targets
0.01Suggestive
colorectal cancerOpen Targets
0.01Suggestive
acute quadriplegic myopathyOpen Targets
0.00Suggestive
Central precocious pubertyOpen Targets
0.00Suggestive
pancreatic ductal adenocarcinomaOpen Targets
0.00Suggestive
breast cancerOpen Targets
0.00Suggestive
posterior cortical atrophyOpen Targets
0.00Suggestive
epilepsyOpen Targets
0.00Suggestive
metastatic melanomaOpen Targets
0.00Suggestive
Dandy-Walker syndromeOpen Targets
0.00Suggestive
Neurodevelopmental disorderOpen Targets
0.00Suggestive
VentriculomegalyOpen Targets
0.00Suggestive
Intellectual developmental disorder, X-linked 103UniProt
Pathogenic Variants3
NM_030624.3(KLHL15):c.1105C>T (p.Arg369Cys)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 369
NM_030624.3(KLHL15):c.1474G>A (p.Val492Ile)Likely pathogenic
Abnormal brain morphology
β˜…β˜†β˜†β˜†β†’ Residue 492
NM_030624.3(KLHL15):c.1179del (p.Tyr394fs)Pathogenic
Intellectual disability, X-linked 103
β˜†β˜†β˜†β˜†2021β†’ Residue 394
View on ClinVar β†—
Related Genes
RBBP8Protein interaction86%MAGEF1Shared pathway67%SPSB1Shared pathway67%KLHL8Shared pathway67%PSMF1Shared pathway50%SPSB2Shared pathway50%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
11%
Liver
8%
Ovary
7%
Heart
6%
Lung
4%
Gene Interaction Network
Click a node to explore
KLHL15RBBP8MAGEF1SPSB1KLHL8PSMF1SPSB2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96M94
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.16Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.03 [0.01–0.16]
RankingsWhere KLHL15 stands among ~20K protein-coding genes
  • #10,341of 20,598
    Most Researched39
  • #4,091of 5,498
    Most Pathogenic Variants3
  • #264of 17,882
    Most Constrained (LOEUF)0.16 Β· top 5%
Genes detectedKLHL15
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.
PMID: 25644381
Mol Psychiatry Β· 2016
1.00
2
VGLL3 modulates chemosensitivity through promoting DNA double-strand break repair.
PMID: 39383226
Sci Adv Β· 2024
0.90
3
The X-linked intellectual disability gene product and E3 ubiquitin ligase KLHL15 degrades doublecortin proteins to constrain neuronal dendritogenesis.
PMID: 33199366
J Biol Chem Β· 2021
0.80
4
Identification and characterization of a novel kelch-like gene KLHL15 in silico.
PMID: 15870933
Oncol Rep Β· 2005
0.70
5
[Clinical features and genetic analysis of 17 Chinese pedigrees affected with X-linked intellectual disability].
PMID: 38684296
Zhonghua Yi Xue Yi Chuan Xue Za Zhi Β· 2024
0.60