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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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KLHDC3
kelch domain containing 3
Chromosome 6 · 6p21.1
NCBI Gene: 116138Ensembl: ENSG00000124702.20HGNC: HGNC:20704UniProt: Q9BQ90
42PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
chromatin bindingprotein bindingubiquitin-like ligase-substrate adaptor activitycytoplasminfectionnon-small cell lung carcinomaovarian cancerobesity
✦AI Summary

KLHDC3 is a substrate-recognition component of the CRL2 E3 ubiquitin ligase complex that mediates protein degradation through the DesCEND (destruction via C-end degrons) pathway 12. The CRL2(KLHDC3) complex specifically recognizes proteins bearing C-terminal degrons—peptide motifs at the extreme C-terminus—particularly those with glycine as the terminal residue and containing preceding arginine residues (e.g., -Arg-(Xaa)n-Arg-Gly, -Arg-(Xaa)n-Lys-Gly motifs) 12. Structurally, KLHDC3 contains a pre-formed pocket within its β-propeller domain that establishes substrate selectivity preferences 3. The complex mediates ubiquitination of truncated selenoproteins (SELENOV, SEPHS2) produced by failed UGA/Sec decoding 4. Clinically, KLHDC3 has emerged as a significant oncoprotein. In non-small cell lung cancer, elevated KLHDC3 expression correlates with worse survival and promotes degradation of the tumor suppressor p14ARF through CUL2-mediated ubiquitination 5. KLHDC3 upregulation contributes to EGFR-targeted drug resistance, suggesting therapeutic potential as a resistance mechanism target 5. In pancreatic cancer, KLHDC3 cooperates with Fbxw7 to promote c-Myc degradation in GSK3-insensitive cells, with KLHDC3 expression associated with patient prognosis in low-SHISA2 tumors 6. Additionally, KLHDC3 loss-of-function rescues proliferation defects in RECQL4-mutant cells by stabilizing truncated RECQL4 variants 7, and rare KLHDC3 variants are associated with familial multiple myeloma 8.

Sources cited
1
KLHDC3 is a substrate-recognition component of CRL2 E3 ubiquitin ligase recognizing C-degrons in the DesCEND pathway
PMID: 29775578
2
CRL2(KLHDC3) recognizes C-terminal glycine-ending degrons with specific preceding arginine/lysine/glutamine motifs
PMID: 29779948
3
CRL2(KLHDC3) mediates ubiquitination and degradation of truncated selenoproteins SELENOV and SEPHS2
PMID: 26138980
4
KLHDC3 contains a pre-formed pocket in its β-propeller establishing preference for Arg or Gln preceding C-terminal Gly
PMID: 39548056
5
KLHDC3 overexpression in NSCLC correlates with worse survival and promotes p14ARF degradation; elevated in EGFR-targeted drug-resistant cells
PMID: 35468939
6
KLHDC3 cooperates with Fbxw7 to promote c-Myc degradation in GSK3-insensitive pancreatic cancer; associated with prognosis
PMID: 38698266
7
KLHDC3 loss stabilizes truncated RECQL4 containing neo-degron sequences, rescuing proliferation defects in RECQL4-mutant cells
PMID: 40777487
8
KLHDC3 variants are identified as candidate disease-causing genes in familial multiple myeloma
PMID: 39947961
Disease Associationsⓘ20
infectionOpen Targets
0.02Suggestive
non-small cell lung carcinomaOpen Targets
0.01Suggestive
ovarian cancerOpen Targets
0.01Suggestive
obesityOpen Targets
0.01Suggestive
acute quadriplegic myopathyOpen Targets
0.01Suggestive
chronic kidney diseaseOpen Targets
0.00Suggestive
Bone marrow hypocellularityOpen Targets
0.00Suggestive
neoplasmOpen Targets
0.00Suggestive
gestational diabetesOpen Targets
0.00Suggestive
cancerOpen Targets
0.00Suggestive
azoospermiaOpen Targets
0.00Suggestive
Alzheimer diseaseOpen Targets
0.00Suggestive
lung cancerOpen Targets
0.00Suggestive
dermatomyositisOpen Targets
0.00Suggestive
viral diseaseOpen Targets
0.00Suggestive
hepatocellular carcinomaOpen Targets
0.00Suggestive
astrocytomaOpen Targets
0.00Suggestive
Rothmund-Thomson syndromeOpen Targets
0.00Suggestive
gastric cancerOpen Targets
0.00Suggestive
Uterine CarcinosarcomaOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
CUL2Protein interaction95%ZER1Protein interaction95%GLMNProtein interaction95%PRAMEProtein interaction95%ASB4Protein interaction95%ZYG11BProtein interaction95%
Tissue Expression6 tissues
Brain
100%
Heart
78%
Liver
46%
Bone Marrow
39%
Ovary
39%
Lung
31%
Gene Interaction Network
Click a node to explore
KLHDC3CUL2ZER1GLMNPRAMEASB4ZYG11B
PROTEIN STRUCTURE
Preparing viewer…
PDB9D1Z · 1.88 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.26Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.11 [0.05–0.26]
RankingsWhere KLHDC3 stands among ~20K protein-coding genes
  • #9,894of 20,598
    Most Researched42
  • #807of 17,882
    Most Constrained (LOEUF)0.26 · top 5%
Genes detectedKLHDC3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases.
PMID: 39548056
Nat Commun · 2024
1.00
2
CRL2
PMID: 38698266
Oncogene · 2024
0.90
3
Minute amounts of helicase-deficient truncated RECQL4 are sufficient for DNA replication.
PMID: 40777487
bioRxiv · 2025
0.80
4
Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2.
PMID: 39396041
Nat Commun · 2024
0.70
5
How kelch domain-containing protein 3 distinguishes between the C-end degron of herpesviral protein UL49.5 and its mutants - Insights from molecular dynamics.
PMID: 38878709
Bioorg Med Chem · 2024
0.60