SCAND3

Chr 6

SCAN domain containing 3

Also known as: Buster4, FAM200D, ZBED9, ZFP38-L, ZNF305P2, ZNF452, dJ1186N24.3

NCBI Gene: 114821ENSG00000232040UniProt: Q6R2W3

Predicted to enable nucleic acid binding activity. Involved in positive regulation of cell cycle and positive regulation of epithelial cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

83
ClinVar variants
5
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SCAND3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
5 Pathogenic / Likely Pathogenic· 75 VUS of 83 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.67LOEUF
pLI 0.000
Z-score 3.36
OE 0.47 (0.34–0.67)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.39Z-score
OE missense 0.74 (0.69–0.80)
495 obs / 668.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.47 (0.34–0.67)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.74 (0.69–0.80)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.80
0≤1.21.6
LoF obs/exp: 22 / 46.8Missense obs/exp: 495 / 668.9Syn Z: 2.42

ClinVar Variant Classifications

83 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
Likely Pathogenic1
VUS75
Likely Benign3
4
Pathogenic
1
Likely Pathogenic
75
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
1
0
1
VUS
0
74
1
0
75
Likely Benign
0
2
0
1
3
Benign
0
0
0
0
0
Total0766183

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SCAND3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
DNA methylation profiles and cancer in children conceived after assisted reproductive technology.
Ducreux B et al.·Clin Epigenetics
2025
Characterizing the mutational landscape of sinonasal squamous cell carcinoma using whole-exome sequencing.
Vareta JA et al.·Oral Oncol
2025
Novel genetic locus at MHC region for esophageal squamous cell carcinoma in Chinese populations.
Zhang P et al.·PLoS One
2017
Sex-stratified Genomic Structural Equation Models of Posttraumatic Stress Inform PTSD Etiology: L'utilisation de la modélisation génomique par équations structurelles stratifiée par sexe du stress post-traumatique pour expliquer l'étiologie du TSPT.
Moo-Choy A et al.·Can J Psychiatry
2025Functional
Comparative analysis of the recently discovered hAT transposon TcBuster in human cells.
Woodard LE et al.·PLoS One
2012
The AGT epistasis pattern proposed a novel role for ZBED9 in regulating blood pressure: Tehran Cardiometabolic genetic study (TCGS).
Akbarzadeh M et al.·Gene
2022
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools