SCGB1A1

Chr 11

secretoglobin family 1A member 1

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

NCBI Gene: 7356 ENSG00000149021 UniProt: P11684

The encoded secretoglobin protein binds phosphatidylcholine and other lipids and serves as a potent inhibitor of phospholipase A2, with anti-inflammatory properties. Mutations in this gene are associated with increased susceptibility to asthma. This gene is not highly constrained against loss-of-function variants, suggesting tolerance to reduced protein levels.

ResearchSummary from RefSeq, UniProt

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]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.92

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

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?

0.15Z-score

OE missense 0.94 (0.75–1.20)

48 obs / 51.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.34 (0.60–1.92)

0≤0.351.4

Missense OE?0.94 (0.75–1.20)

0≤0.61.4

Synonymous OE?1.15

0≤1.21.6

LoF obs/exp: 4 / 3.0Missense obs/exp: 48 / 51.0Syn Z: -0.52

Background carrier burden — how many people carry a rare variant somewhere in SCGB1A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 980

124 rare PASS variants

Rare truncating (LoF)

1 in 970

30 rare PASS variants

Rare synonymous (reference)

1 in 1,600

46 rare PASS variants

Rare missense and truncating variants are carried at similar rates in SCGB1A1; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 1,500	1 in 5,100
South Asian	~43k	1 in 320	1 in 4,700
Remaining (unassigned)	~30k	1 in 630	1 in 620
European (Finnish)	~27k	1 in 3,800	1 in 1,100
Admixed American	~22k	1 in 500	1 in 530
African / African American	~21k	1 in 1,100	1 in 2,900
East Asian	~20k	1 in 250	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 1,900	none seen
Middle Eastern	~2,884	1 in 290	≈ 1 in 960

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.