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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SCAF1
SR-related CTD associated factor 1
Chromosome 19 · 19q13.33
NCBI Gene: 58506Ensembl: ENSG00000126461.16HGNC: HGNC:30403UniProt: Q9H7N4
70PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA polymerase II C-terminal domain bindingprotein bindingmRNA processingnucleusneurodegenerative diseaseautism spectrum disorderskin cancerbasal cell carcinoma
✦AI Summary

SCAF1 (SR-related CTD associated factor 1) is a multifunctional protein that plays critical roles in transcriptional regulation and mitochondrial bioenergetics. As a member of the SR superfamily of pre-mRNA splicing factors, SCAF1 interacts with the C-terminal domain of RNA polymerase II and functions as a critical activator of RNA polymerase II elongation and global transcription 12. Mechanistically, SCAF1 depletion leads to RNA polymerase II stalling at GC-rich regions within gene bodies, resulting in decreased RNA synthesis and increased proteasomal degradation of stalled polymerase complexes 2. Beyond transcriptional regulation, SCAF1 serves as a supercomplex assembly factor (also known as COX7A2L) that promotes formation of mitochondrial respiratory chain supercomplexes, enhancing oxidative phosphorylation and ATP production 34. The protein is upregulated by the PERK-eIF2α-ATF4 pathway during ER stress and nutrient deprivation 3. Clinically, SCAF1 has significant disease relevance as a moderate-risk gene for autism spectrum disorders 5, a potential tumor suppressor in pancreatic cancer 6, and shows altered expression in focal segmental glomerulosclerosis 7. Loss of SCAF1 affects cellular metabolism by increasing glutamine dependency and promoting anabolic pathways 4, making it a potential therapeutic target in metabolic diseases and cancer.

Sources cited
1
SCAF1 is a member of the SR superfamily of pre-mRNA splicing factors that interacts with RNA polymerase II CTD
PMID: 29787824
2
SCAF1 is a critical activator of RNAPII elongation and global transcription, with depletion causing RNAPII stalling
PMID: 39698826
3
SCAF1 functions as a supercomplex assembly factor promoting mitochondrial respiratory chain supercomplexes and is upregulated by PERK-eIF2α-ATF4 pathway
PMID: 31023583
4
SCAF1 depletion affects cellular metabolism by increasing glutamine dependency and promoting anabolic pathways
PMID: 37351168
5
SCAF1 is identified as a new moderate-risk gene for autism spectrum disorders
PMID: 35982159
6
SCAF1 functions as a tumor suppressor in pancreatic cancer
PMID: 38902237
7
SCAF1 shows altered expression in focal segmental glomerulosclerosis
PMID: 31308072
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.43Moderate
autism spectrum disorderOpen Targets
0.09Suggestive
skin cancerOpen Targets
0.09Suggestive
basal cell carcinomaOpen Targets
0.07Suggestive
thyroid diseaseOpen Targets
0.06Suggestive
Hashimoto's thyroiditisOpen Targets
0.06Suggestive
schizophreniaOpen Targets
0.05Suggestive
hypertensionOpen Targets
0.04Suggestive
cutaneous melanomaOpen Targets
0.04Suggestive
cardiovascular diseaseOpen Targets
0.04Suggestive
mathematical abilityOpen Targets
0.03Suggestive
neoplasmOpen Targets
0.03Suggestive
Increased blood pressureOpen Targets
0.03Suggestive
hypothyroidismOpen Targets
0.03Suggestive
Chest painOpen Targets
0.03Suggestive
Malignant Pancreatic NeoplasmOpen Targets
0.03Suggestive
cancerOpen Targets
0.02Suggestive
VitiligoOpen Targets
0.02Suggestive
dry eye syndromeOpen Targets
0.02Suggestive
CirrhosisOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ERFProtein interaction82%REXO1Protein interaction82%PRR12Protein interaction80%NACC1Protein interaction79%PTPN23Protein interaction73%GLIS3Shared pathway50%
Tissue Expression6 tissues
Brain
100%
Ovary
98%
Liver
88%
Lung
81%
Heart
40%
Bone Marrow
35%
Gene Interaction Network
Click a node to explore
SCAF1ERFREXO1PRR12NACC1PTPN23GLIS3
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt Q9H7N4
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.55Moderately Constrained
pLIⓘ
0.40Tolerant
Observed/Expected LoF0.40 [0.30–0.55]
RankingsWhere SCAF1 stands among ~20K protein-coding genes
  • #6,758of 20,598
    Most Researched70
  • #3,556of 17,882
    Most Constrained (LOEUF)0.55 · top quartile
Genes detectedSCAF1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes.
PMID: 35982159
Nat Genet · 2022
1.00
2
Contributions of Rare Gene Variants to Familial and Sporadic FSGS.
PMID: 31308072
J Am Soc Nephrol · 2019
0.90
3
ER and Nutrient Stress Promote Assembly of Respiratory Chain Supercomplexes through the PERK-eIF2α Axis.
PMID: 31023583
Mol Cell · 2019
0.80
4
Targeting SOX13 inhibits assembly of respiratory chain supercomplexes to overcome ferroptosis resistance in gastric cancer.
PMID: 38769295
Nat Commun · 2024
0.70
5
In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer.
PMID: 38902237
Nat Commun · 2024
0.60