SCGB3A2
protein-codingsecretoglobin family 3A member 2, the group of Secretoglobins
Gene summary
The protein encoded by this gene is a secreted lung surfactant protein and a downstream target of thyroid transcription factor. A single nucleotide polymorphism in the promoter of this gene results in susceptibility to asthma.[provided by RefSeq, Mar 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SCGB3A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_054023.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 | 13 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_473364.1 | 3 | MANE Select | |
| Ensembl | ENSP00000296694.4 | 3 | MANE Select | |
| Ensembl | ENSP00000423930.1 | 2 | Standard | |
| Ensembl | ENSP00000423930.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Binding and Uptake of Ligands by Scavenger Receptors
- Scavenging by Class A Receptors
Biological Process
- receptor-mediated endocytosis
Cellular Component
- extracellular region
- extracellular space
- endocytic vesicle lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296694
- Coding exons
- 3
- Length
- 11510
- Individuals with no LoFs
- 125680
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 23
- Defined
- 125704
- p
- 0.0000955
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.111 | 44 | 46.1 | 0.954 | 0.00000202 | 587 |
| Missense (PolyPhen) | 16 | 15.453 | 1.0354 | 192 | ||
| Synonymous | 0.835 | 15 | 19.7 | 0.761 | 9.26e-7 | 202 |
| Loss of Function | -0.0465 | 3 | 2.91 | 1.03 | 1.21e-7 | 42 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.00026 | 0.00023 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Secreted cytokine-like protein (PubMed:12847263). Binds to the scavenger receptor MARCO (PubMed:12847263). Can also bind to pathogens including the Gram-positive bacterium L.monocytogenes, the Gram-negative bacterium P.aeruginosa, and yeast (PubMed:12847263). Strongly inhibits phospholipase A2 (PLA2G1B) activity (PubMed:24213919). Seems to have anti- inflammatory effects in respiratory epithelium (By similarity). Also has anti-fibrotic activity in lung (PubMed:24213919). May play a role in fetal lung development and maturation (PubMed:24213919). Promotes branching morphogenesis during early stages of lung development (PubMed:24213919). In the pituitary, may inhibit production of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) (By similarity). {ECO:0000250|UniProtKB:Q920H1, ECO:0000269|PubMed:12847263, ECO:0000269|PubMed:24213919}.;
Recessive Scores
- pRec
- 0.0300
Intolerance Scores
- LoFtool
- 0.626
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.04
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.844
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |