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4 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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KHDC4
KH domain containing 4, pre-mRNA splicing factor
Chromosome 1 · 1q22
NCBI Gene: 22889Ensembl: ENSG00000132680.12HGNC: HGNC:29145UniProt: Q7Z7F0
38PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
spliceosomal complexRNA bindingprotein bindingmRNA splice site recognitionAbnormality of the skeletal systemspinal stenosisrhabdomyolysisatrial fibrillation
✦AI Summary

KHDC4 (KH domain containing 4) is an RNA-binding protein functioning as a pre-mRNA splicing factor. It contains KH domains that mediate preferential binding to A/C-rich sequences and poly-C stretches in RNA 1. KHDC4 interacts with the PRP19C/Prp19 complex (NTC/Nineteen complex), a core spliceosomal component involved in the second catalytic step of splicing and spliceosome assembly 2. The protein regulates splice site selection, with overexpression altering both 5' and 3' splice site utilization 2. Clinically, KHDC4 exhibits significant disease relevance in cancer. In prostate cancer, KHDC4 expression is elevated in late-stage and lymph node metastatic tumors, positively correlating with poor overall and disease-free survival 3. The KHDC4-TRAF2 axis contributes to tumor malignancy features, with KHDC4/TRAF2 distribution showing superior prognostic correlation with Gleason score compared to PSA 3. In breast cancer, KHDC4 functions as a potential miR-641 target within a ceRNA regulatory network, with miR-641 overexpression inhibiting cell proliferation and invasion 4. These findings suggest KHDC4 may serve as a prognostic biomarker for advanced cancer and a potential therapeutic target.

Sources cited
1
KHDC4 (Blom7alpha) interacts with SNEV/Prp19/Pso4 complex, regulates splice site selection, and increases splicing activity in dose-dependent manner
PMID: 19641227
2
KHDC4 (Blom7alpha) binds preferentially to A/C-rich sequences and poly-C stretches; its RNA binding activity is required for pre-mRNA splicing catalysis
PMID: 23144703
3
KHDC4 is elevated in late-stage prostate cancer and lymph node metastasis, correlates with poor overall and disease-free survival, and functions in KHDC4-TRAF2 axis contributing to tumor malignancy
PMID: 40560737
4
KHDC4 is a potential target of miR-641 in breast cancer; miR-641 overexpression inhibits cell proliferation and invasion
PMID: 35152838
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
Abnormality of the skeletal systemOpen Targets
0.26Weak
spinal stenosisOpen Targets
0.20Weak
rhabdomyolysisOpen Targets
0.18Weak
atrial fibrillationOpen Targets
0.15Weak
oral squamous cell carcinomaOpen Targets
0.08Suggestive
posterior cortical atrophyOpen Targets
0.07Suggestive
Parkinson diseaseOpen Targets
0.06Suggestive
neoplasmOpen Targets
0.04Suggestive
prostate cancerOpen Targets
0.02Suggestive
infectious meningitisOpen Targets
0.02Suggestive
prostate adenocarcinomaOpen Targets
0.02Suggestive
cancerOpen Targets
0.02Suggestive
colorectal carcinomaOpen Targets
0.01Suggestive
non-small cell lung carcinomaOpen Targets
0.01Suggestive
ovarian carcinomaOpen Targets
0.01Suggestive
lymph node metastatic carcinomaOpen Targets
0.01Suggestive
melanomaOpen Targets
0.01Suggestive
ataxia telangiectasiaOpen Targets
0.01Suggestive
chronic kidney diseaseOpen Targets
0.01Suggestive
lung adenocarcinomaOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
LUC7LShared pathway100%LUC7L2Shared pathway100%CELF6Shared pathway50%CELF5Shared pathway50%LUC7L3Shared pathway50%PUF60Shared pathway33%
Tissue Expression6 tissues
Ovary
100%
Lung
68%
Liver
61%
Bone Marrow
49%
Heart
40%
Brain
27%
Gene Interaction Network
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KHDC4LUC7LLUC7L2CELF6CELF5LUC7L3PUF60
PROTEIN STRUCTURE
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PDB2YQR · NMR
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.41Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.27 [0.18–0.41]
RankingsWhere KHDC4 stands among ~20K protein-coding genes
  • #10,499of 20,598
    Most Researched38
  • #2,122of 17,882
    Most Constrained (LOEUF)0.41 · top quartile
Genes detectedKHDC4
Sources retrieved4 papers
Response time—
📄 Sources
4
1
LINC00665 sponges miR-641 to promote the progression of breast cancer by targeting the SNF2-related CREBBP activator protein (SRCAP).
PMID: 35152838
Bioengineered · 2022
1.00
2
Implications of the KHDC4-TRAF2 axis in the context of prostate cancer prognosis.
PMID: 40560737
Aging (Albany NY) · 2025
0.75
3
Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA.
PMID: 23144703
PLoS One · 2012
0.50
4
Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4.
PMID: 19641227
J Biol Chem · 2009
0.25