| Evidence type | Key finding | Quantitative/statistical details | Study/citation (include DOI URL and publication date) | Notes/limitations |
|---|---|---|---|---|
| Proteomics detectability | SCGB1C2 is difficult/impossible to validate by mass spectrometry because its tryptic peptides are not unique and overlap with SCGB1C1; the gene is described as being completely subsumed by SCGB1C1 for peptide evidence. (pqac-00000000, pqac-00000006) | “All of SCGB1C2’s tryptic peptides of length at least 9 aa overlap with variants of SCGB1C1”; alternative proteases were considered, but “MS with any protease does not seem fruitful” for such cases. (pqac-00000000, pqac-00000006) | Siddiqui O, Zhang H, Guan Y, Omenn GS. *Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge.* **Journal of Proteome Research**. Publication date: Oct 2018. DOI: 10.1021/acs.jproteome.8b00442. URL: https://doi.org/10.1021/acs.jproteome.8b00442 (pqac-00000000, pqac-00000006) | Evidence is negative/technical rather than functional. The main issue is SCGB1C2 vs SCGB1C1 peptide non-uniqueness, so absence of MS confirmation does **not** prove absence of expression. |
| Differential abundance in nasal lavage proteomics | The retrieved CRSwNP nasal lavage proteomics study reported **SCGB1C1**, not SCGB1C2, among top dysregulated proteins; no SCGB1C2 entry was found in the visible table/document search. (pqac-00000003, pqac-00000005, pqac-00000007, pqac-00000008) | For **SCGB1C1**: coverage 40%; abundance ratio (CRSwNP)/(CONTROL) = -18.52; log2 abundance ratio = -4.22; p = 0.00276391; adjusted p = 0.0319461. Study significance cutoffs: FDR p ≤ 0.05 and fold change ≥ 1.5. (pqac-00000003, pqac-00000005) | Kashoob M, Masood A, Alfadda AA, et al. *Label-Free Quantitative Proteomics Analysis of Nasal Lavage Fluid in Chronic Rhinosinusitis with Nasal Polyposis.* **Biology**. Publication date: Oct 2024. DOI: 10.3390/biology13110887. URL: https://doi.org/10.3390/biology13110887 (pqac-00000003, pqac-00000005) | This is a key ambiguity trap: the study supports differential abundance of **SCGB1C1**, not SCGB1C2. It should not be used as direct evidence for SCGB1C2. |
| Disease association evidence from OpenTargets | OpenTargets lists low-to-moderate disease associations for SCGB1C2, including cataract-related traits, lens disease, chronic fatigue syndrome, and glomerulonephritis. (pqac-00000004) | Evidence sizes reported as 3 for each listed disease. Scores shown in the context: lens disease 0.41214602983498017; cataract 0.3776757400496717; senile cataract 0.29767603147254373; chronic fatigue syndrome 0.036558074682322375; glomerulonephritis 0.0258484070613862. Underlying literature listed as PMID 40770095. (pqac-00000004) | OpenTargets search result for SCGB1C2 / ENSG00000268320. Context provides disease-target association output and PMID linkage; no DOI/URL for the underlying paper was available in the provided context. Retrieved during this session. (pqac-00000004) | These are database-derived associations, not necessarily direct mechanistic validation. Because only the OpenTargets summary was available here, interpretation should be cautious until the underlying PMID 40770095 is reviewed directly. |


*Table: This table compiles the specific SCGB1C2 evidence available in the retrieved context, separating true SCGB1C2 findings from frequent SCGB1C1-related ambiguity. It is useful for showing that direct functional literature is limited and that proteomics evidence is constrained by sequence overlap.*