SCGB1A1
Basic information
Region (hg38): 11:62405102-62423195
Previous symbols: [ "UGB" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB1A1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 2 | 1 |
Variants in SCGB1A1
This is a list of pathogenic ClinVar variants found in the SCGB1A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-62419058-G-G | Inherited susceptibility to asthma | Uncertain significance (Jul 01, 2002) | ||
| 11-62419070-G-A | Chronic obstructive pulmonary disease | association (Feb 03, 2021) | ||
| 11-62422221-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 11-62422239-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 11-62422240-G-A | Likely benign (Dec 13, 2017) | |||
| 11-62422264-C-T | Benign (Jan 19, 2018) | |||
| 11-62422302-T-C | not specified | Uncertain significance (May 16, 2024) | ||
| 11-62422407-T-C | not specified | Likely benign (Jan 03, 2024) | ||
| 11-62423081-T-C | not specified | Uncertain significance (Dec 30, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCGB1A1 | protein_coding | protein_coding | ENST00000278282 | 3 | 18093 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000799 | 0.342 | 124089 | 0 | 1 | 124090 | 0.00000403 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.149 | 48 | 51.0 | 0.941 | 0.00000265 | 596 |
| Missense in Polyphen | 13 | 12.629 | 1.0293 | 148 | ||
| Synonymous | -0.521 | 22 | 19.1 | 1.15 | 0.00000102 | 176 |
| Loss of Function | -0.543 | 4 | 2.99 | 1.34 | 1.26e-7 | 38 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000892 | 0.00000892 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds phosphatidylcholine, phosphatidylinositol, polychlorinated biphenyls (PCB) and weakly progesterone, potent inhibitor of phospholipase A2.;
- Pathway
- Prostaglandin Synthesis and Regulation;FOXA1 transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.258
Intolerance Scores
- loftool
- 0.686
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.0730
- hipred
- N
- hipred_score
- 0.310
- ghis
- 0.435
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.733
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scgb1a1
- Phenotype
- immune system phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; neoplasm; respiratory system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;signal transduction;female pregnancy;embryo implantation;response to xenobiotic stimulus;response to ozone;response to lipopolysaccharide;negative regulation of interferon-gamma production;negative regulation of interleukin-13 production;negative regulation of interleukin-4 production;negative regulation of interleukin-5 production;response to silicon dioxide;response to cytokine;negative regulation of T cell proliferation;negative regulation of catalytic activity;regulation of mRNA stability;regulation of inflammatory response;response to glucocorticoid;response to fibroblast growth factor
- Cellular component
- extracellular space;nuclear envelope;cytoplasm;rough endoplasmic reticulum;secretory granule;extracellular exosome
- Molecular function
- protein binding;phospholipase A2 inhibitor activity;polychlorinated biphenyl binding