SCGB1A1

Chr 11

secretoglobin family 1A member 1

Also known as: CC10, CC16, CCPBP, CCSP, UGB, UP-1, UP1

NCBI Gene: 7356ENSG00000149021UniProt: P11684

This gene encodes a member of the secretoglobin family of small secreted proteins. The encoded protein has been implicated in numerous functions including anti-inflammation, inhibition of phospholipase A2 and the sequestering of hydrophobic ligands. Defects in this gene are associated with a susceptibility to asthma. [provided by RefSeq, May 2010]

22
ClinVar variants
9
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SCGB1A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
9 Pathogenic / Likely Pathogenic· 10 VUS of 22 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.
1.92LOEUF
pLI 0.001
Z-score -0.54
OE 1.34 (0.60–1.92)
Tolerant

Highly tolerant — LoF variants common in population

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.
0.15Z-score
OE missense 0.94 (0.75–1.20)
48 obs / 51.0 exp
Tolerant

Mild missense constraint

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.1.34 (0.60–1.92)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.94 (0.75–1.20)
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.1.15
0≤1.21.6
LoF obs/exp: 4 / 3.0Missense obs/exp: 48 / 51.0Syn Z: -0.52

ClinVar Variant Classifications

22 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
Likely Pathogenic3
VUS10
Likely Benign2
Benign1
6
Pathogenic
3
Likely Pathogenic
10
VUS
2
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
3
0
3
VUS
0
5
5
0
10
Likely Benign
0
1
0
1
2
Benign
0
0
0
1
1
Total0614222

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

View in ClinVar →

Protein Context — Lollipop Plot

SCGB1A1 · 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
Lung Tissue Multilayer Network Analysis Uncovers the Molecular Heterogeneity of Chronic Obstructive Pulmonary Disease.
Olvera N et al.·Am J Respir Crit Care Med
2024
Mouse models of lung-specific SARS-CoV-2 infection with moderate pathological traits.
Kim SH et al.·Front Immunol
2022Functional
SCGB1A1 rs3741240 variant downregulates CC16: a molecular insight into COPD pathogenesis in Indian population.
Sultana N et al.·Front Immunol
2025
Club Cell Loss as a Feature of Bronchiolization in ILD.
Reynaud P et al.·Front Immunol
2021Clinical trial
Dysregulation of club cell biology in idiopathic pulmonary fibrosis.
Zuo WL et al.·PLoS One
2020
Sputum Proteomics in Nontuberculous Mycobacterial Lung Disease.
Hull RC et al.·Chest
2022
Ontogeny and Biology of Human Small Airway Epithelial Club Cells.
Zuo WL et al.·Am J Respir Crit Care Med
2018
Edaravone alleviates Pseudomonas aeruginosa associated-acute lung injury by inhibiting inflammation and promoting anti-microbial peptide production.
Song J et al.·Int Immunopharmacol
2025
Non-invasive assessment of small airway remodelling in smokers.
Bourdin A et al.·COPD
2010Functional
Transcriptional analysis identifies potential novel biomarkers associated with successful ex-vivo perfusion of human donor lungs.
Ferdinand JR et al.·Clin Transplant
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