SCGB1D2

Chr 11

secretoglobin family 1D member 2

ENSG00000124935 UniProt: O95969 OMIM: 615061

The protein encoded by this gene is a lipophilin that may bind androgens and other steroids and appears to be transcriptionally regulated by steroid hormones. No established Mendelian disease associations have been reported for mutations in this gene based on the available information. The gene shows moderate tolerance to loss-of-function variants with a pLI of 0.27 and LOEUF of 1.27.

OMIM ResearchSummary from RefSeq, UniProt

May bind androgens and other steroids, may also bind estramustine, a chemotherapeutic agent used for prostate cancer. May be under transcriptional regulation of steroid hormones

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.27

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

ncbi: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.27LOEUF

pLI 0.270

Z-score 1.28

OE 0.27 (0.10–1.27)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.38Z-score

OE missense 1.16 (0.93–1.45)

55 obs / 47.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.27 (0.10–1.27)

0≤0.351.4

Missense OE?1.16 (0.93–1.45)

0≤0.61.4

Synonymous OE?1.19

0≤1.21.6

LoF obs/exp: 1 / 3.6Missense obs/exp: 55 / 47.6Syn Z: -0.67

Background carrier burden — how many people carry a rare variant somewhere in SCGB1D2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 250

120 rare PASS variants

Rare truncating (LoF)

1 in 10,000

26 rare PASS variants

Rare synonymous (reference)

1 in 840

45 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SCGB1D2. 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 280	1 in 10,000
South Asian	~43k	1 in 580	1 in 2,300
Remaining (unassigned)	~30k	1 in 160	1 in 6,000
European (Finnish)	~27k	1 in 1,300	none seen
Admixed American	~22k	1 in 380	≈ 1 in 22,000
African / African American	~21k	1 in 230	≈ 1 in 8,400
East Asian	~20k	1 in 1,200	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 1,900	none seen
Middle Eastern	~2,884	1 in 260	none seen

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 ↓