SCGB1D4

Chr 11

secretoglobin family 1D member 4

ENSG00000197745 UniProt: Q6XE38 OMIM: 615062

The protein is predicted to regulate chemotactic cell migration and invasion in the extracellular space. Currently, no definitive disease associations have been established for mutations in this gene. The gene shows low constraint to loss-of-function variation, suggesting it may be tolerant to mutations.

OMIM ResearchSummary from RefSeq, UniProt

Seems to be involved in the regulation of chemotactic cell migration and invasion

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.60

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?

1.60LOEUF

pLI 0.057

Z-score 0.78

OE 0.56 (0.22–1.60)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.67Z-score

OE missense 0.71 (0.54–0.96)

31 obs / 43.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.56 (0.22–1.60)

0≤0.351.4

Missense OE?0.71 (0.54–0.96)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 2 / 3.6Missense obs/exp: 31 / 43.4Syn Z: -0.02

Background carrier burden — how many people carry a rare variant somewhere in SCGB1D4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 520

95 rare PASS variants

Rare truncating (LoF)

1 in 5,300

30 rare PASS variants

Rare synonymous (reference)

1 in 3,400

38 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SCGB1D4. 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 1,100	1 in 7,000
South Asian	~43k	1 in 1,100	1 in 5,400
Remaining (unassigned)	~30k	1 in 550	1 in 4,300
European (Finnish)	~27k	1 in 4,400	≈ 1 in 27,000
Admixed American	~22k	1 in 520	1 in 2,800
African / African American	~21k	1 in 730	1 in 1,800
East Asian	~20k	1 in 620	1 in 980
Ashkenazi Jewish	~13k	≈ 1 in 6,500	none seen
Middle Eastern	~2,884	1 in 260	≈ 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 ↓