SCGB3A2

secretoglobin family 3A member 2, the group of Secretoglobins

Basic information

Region (hg38): 5:147870682-147882191

Links

ENSG00000164265 ∙ NCBI:117156 ∙ OMIM:606531 ∙ HGNC:18391 ∙ Uniprot:Q96PL1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCGB3A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB3A2 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in SCGB3A2

This is a list of pathogenic ClinVar variants found in the SCGB3A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-147878599-G-A		Inherited susceptibility to asthma	risk factor (Mar 01, 2002)
5-147881517-C-A		not specified	Uncertain significance (Apr 27, 2024)
5-147881541-C-G		not specified	Uncertain significance (Oct 05, 2022)
5-147881556-C-A		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB3A2	protein_coding	protein_coding	ENST00000296694	3	11510

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00611	0.516	125680	1	23	125704	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.111	44	46.1	0.954	0.00000202	587
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000324	0.000323
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000262	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Vesicle-mediated transport;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors (Consensus)

Recessive Scores

• pRec: 0.0300

Intolerance Scores

• loftool: 0.626
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.0203
• hipred: N
• hipred_score: 0.123
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.844

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Low	Medium

Mouse Genome Informatics

• Gene name: Scgb3a2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis
• Cellular component: extracellular region;extracellular space;endocytic vesicle lumen