SCGB2A2

Chr 11

secretoglobin family 2A member 2

Also known as: MGB1, PSBP1, UGB2

NCBI Gene: 4250 ENSG00000110484 UniProt: Q13296 OMIM: 605562

The protein is predicted to be involved in androgen receptor signaling and functions in the extracellular space. This gene is highly tolerant to loss-of-function variants (LOEUF 1.905), suggesting that complete loss of function may not be pathogenic. No established Mendelian diseases have been definitively linked to mutations in this gene.

OMIM ResearchSummary from RefSeq

Predicted to be involved in androgen receptor signaling pathway. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.91

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.91LOEUF

pLI 0.000

Z-score -0.53

OE 1.29 (0.63–1.91)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.23Z-score

OE missense 0.91 (0.71–1.16)

44 obs / 48.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.29 (0.63–1.91)

0≤0.351.4

Missense OE?0.91 (0.71–1.16)

0≤0.61.4

Synonymous OE?0.99

0≤1.21.6

LoF obs/exp: 5 / 3.9Missense obs/exp: 44 / 48.6Syn Z: 0.04

Background carrier burden — how many people carry a rare variant somewhere in SCGB2A2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 250

183 rare PASS variants

Rare truncating (LoF)

1 in 12,000

29 rare PASS variants

Rare synonymous (reference)

1 in 380

55 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SCGB2A2. 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 360	1 in 21,000
South Asian	~43k	1 in 270	1 in 5,400
Remaining (unassigned)	~30k	1 in 170	≈ 1 in 7,500
European (Finnish)	~27k	1 in 3,300	≈ 1 in 8,900
Admixed American	~22k	1 in 270	1 in 2,700
African / African American	~21k	1 in 200	1 in 1,500
East Asian	~20k	1 in 480	none seen
Ashkenazi Jewish	~13k	1 in 2,200	none seen
Middle Eastern	~2,884	1 in 140	≈ 1 in 1,400

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.

Exome coverage (gnomAD): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓