HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCAF4
SR-related CTD associated factor 4
Chromosome 21 Β· 21q22.11
NCBI Gene: 57466Ensembl: ENSG00000156304.16HGNC: HGNC:19304UniProt: O95104
80PubMed Papers
21Diseases
0Drugs
40Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of termination of RNA polymerase II transcription, poly(A)-coupledRNA bindingRNA polymerase II C-terminal domain phosphoserine bindingnucleusFliedner-Zweier syndromegenetic disordercomplex neurodevelopmental disorderIntellectual disability
✦AI Summary

SCAF4 is an anti-terminator protein essential for regulating mRNA termination during RNA polymerase II (POLR2A) transcription 1. It functions by binding the phosphorylated C-terminal domain (CTD) of POLR2A and subsequently binding nascent RNA upstream of early polyadenylation sites to suppress premature mRNA cleavage and polyadenylation 1. Working redundantly with SCAF8, SCAF4 prevents accumulation of non-functional truncated proteins by suppressing alternative early poly(A) site usage 1. Independently of SCAF8, SCAF4 also suppresses transcriptional readthrough and ensures correct termination at canonical distal sites 1. Pathogenic variants in SCAF4 cause a variable autosomal dominant neurodevelopmental disorder characterized by developmental delay, seizures, intellectual disability, and skeletal abnormalities 23. Disease-causing variants include truncating, splice-site, and missense mutations predominantly affecting the N-terminal two-thirds of the protein 3. SCAF4 deficiency results in broad mRNA processing dysregulation affecting over 9,000 genes and differential splicing of 2,900 genes 2. Additionally, SCAF4 is implicated in cancer biology, with elevated SCAF4-POLR2A interaction contributing to triple-negative breast cancer progression 4.

Sources cited
1
SCAF4 functions as an anti-terminator protein binding phosphorylated POLR2A CTD and suppressing early polyadenylation sites
PMID: 31104839
2
SCAF4 variants cause neurodevelopmental disorder with impaired mRNA processing affecting thousands of genes
PMID: 32730804
3
Further delineation of SCAF4-associated neurodevelopmental disorder with 50 individuals showing truncating, splice-site, and missense variants
PMID: 39668183
4
SCAF4-POLR2A interaction drives triple-negative breast cancer progression and immune regulation
PMID: 40574704
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
Fliedner-Zweier syndromeOpen Targets
0.72Strong
genetic disorderOpen Targets
0.51Moderate
complex neurodevelopmental disorderOpen Targets
0.50Moderate
Intellectual disabilityOpen Targets
0.43Moderate
Neurodevelopmental disorderOpen Targets
0.41Moderate
Abnormality of the kidneyOpen Targets
0.34Weak
multicystic dysplastic kidneyOpen Targets
0.34Weak
rare syndromic intellectual disabilityOpen Targets
0.34Weak
smoking initiationOpen Targets
0.28Weak
attention deficit hyperactivity disorderOpen Targets
0.27Weak
risk-taking behaviourOpen Targets
0.27Weak
neurodevelopmental disorder with dysmorphic facies and distal limb anomaliesOpen Targets
0.27Weak
substance abuseOpen Targets
0.26Weak
protozoa infectious diseaseOpen Targets
0.26Weak
congenital disorder of glycosylation type IIOpen Targets
0.12Weak
SLC39A8-CDGOpen Targets
0.12Weak
amyotrophic lateral sclerosisOpen Targets
0.04Suggestive
motor neuron diseaseOpen Targets
0.03Suggestive
Atrophy/Degeneration affecting the central nervous systemOpen Targets
0.03Suggestive
male infertilityOpen Targets
0.03Suggestive
Fliedner-Zweier syndromeUniProt
Pathogenic Variants40
NM_020706.2(SCAF4):c.1339C>T (p.Arg447Ter)Pathogenic
not provided|Fliedner-Zweier syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 447
NM_020706.2(SCAF4):c.1471C>T (p.Arg491Ter)Pathogenic
Fliedner-Zweier syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 491
NM_020706.2(SCAF4):c.176del (p.Lys59fs)Pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 59
NM_020706.2(SCAF4):c.1801dup (p.Tyr601fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 601
NM_020706.2(SCAF4):c.1585G>T (p.Glu529Ter)Likely pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 529
NM_020706.2(SCAF4):c.1429C>T (p.Arg477Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 477
NM_020706.2(SCAF4):c.1693C>T (p.Arg565Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 565
NM_020706.2(SCAF4):c.2015del (p.Pro672fs)Pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 672
NM_020706.2(SCAF4):c.656_660dup (p.Asn221fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 221
NM_020706.2(SCAF4):c.30+2delLikely pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2024
NM_020706.2(SCAF4):c.1457_1460del (p.Lys486fs)Pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 486
NM_020706.2(SCAF4):c.1861_1862del (p.Leu621fs)Likely pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 621
NM_020706.2(SCAF4):c.160-1G>ALikely pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2024
NM_020706.2(SCAF4):c.115-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_020706.2(SCAF4):c.1669dup (p.Tyr557fs)Pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 557
NM_020706.2(SCAF4):c.1457_1458del (p.Lys486fs)Likely pathogenic
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
β˜…β˜†β˜†β˜†2023β†’ Residue 486
NM_020706.2(SCAF4):c.294T>G (p.Tyr98Ter)Likely pathogenic
Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 98
NM_020706.2(SCAF4):c.959+1G>TLikely pathogenic
SCAF4-related disorder
β˜…β˜†β˜†β˜†2023
NM_020706.2(SCAF4):c.1889G>A (p.Trp630Ter)Pathogenic
not provided|Fliedner-Zweier syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 630
NM_020706.2(SCAF4):c.1423C>T (p.Arg475Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 475
View on ClinVar β†—
Related Genes
POLR2AProtein interaction93%SETXProtein interaction93%SUPT5HProtein interaction85%PCF11Protein interaction78%NCBP2Protein interaction78%SCAF8Co-mentioned in literature20%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
64%
Liver
60%
Lung
59%
Brain
47%
Heart
37%
Gene Interaction Network
Click a node to explore
SCAF4POLR2ASETXSUPT5HPCF11NCBP2SCAF8
PROTEIN STRUCTURE
Preparing viewer…
PDB6XKB Β· 1.60 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.28Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.19 [0.13–0.28]
RankingsWhere SCAF4 stands among ~20K protein-coding genes
  • #5,963of 20,598
    Most Researched80
  • #1,544of 5,498
    Most Pathogenic Variants40
  • #1,023of 17,882
    Most Constrained (LOEUF)0.28 Β· top 10%
Genes detectedSCAF4
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing.
PMID: 32730804
Am J Hum Genet Β· 2020
1.00
2
Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of esophageal cancer for therapeutic targeting.
PMID: 34400640
Nat Commun Β· 2021
0.90
3
Further delineation of the SCAF4-associated neurodevelopmental disorder.
PMID: 39668183
Eur J Hum Genet Β· 2025
0.80
4
SCAF4-related syndromic intellectual disability.
PMID: 36333968
Am J Med Genet A Β· 2023
0.70
5
PT
PMID: 40574704
Adv Sci (Weinh) Β· 2025
0.60