SCGB3A1

secretoglobin family 3A member 1, the group of Secretoglobins

Basic information

Region (hg38): 5:180590105-180591499

Links

ENSG00000161055 ∙ NCBI:92304 ∙ OMIM:606500 ∙ HGNC:18384 ∙ Uniprot:Q96QR1 ∙ 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 SCGB3A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB3A1 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			4	3		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	3	0

Variants in SCGB3A1

This is a list of pathogenic ClinVar variants found in the SCGB3A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-180590242-C-T		not specified	Likely benign (Oct 24, 2024)
5-180590250-G-A		not specified	Likely benign (Dec 28, 2023)
5-180590632-C-T		not specified	Likely benign (Aug 25, 2024)
5-180590652-G-A		not specified	Uncertain significance (Jan 09, 2024)
5-180590751-A-G		not specified	Uncertain significance (Mar 01, 2024)
5-180590787-G-T		not specified	Likely benign (Feb 19, 2025)
5-180590788-C-T		not specified	Uncertain significance (Feb 19, 2025)
5-180591422-G-A		not specified	Uncertain significance (Mar 02, 2023)
5-180591438-G-A		not specified	Uncertain significance (Sep 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB3A1	protein_coding	protein_coding	ENST00000292641	3	1438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0305	0.613	119158	0	3	119161	0.0000126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.322	38	44.0	0.863	0.00000194	616
Missense in Polyphen		7	6.7016	1.0445		58
Synonymous	0.0672	24	24.4	0.983	0.00000113	250
Loss of Function	0.209	2	2.35	0.853	9.90e-8	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000627	0.0000559
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000627	0.0000559
South Asian	0.0000693	0.0000675
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Secreted cytokine-like protein. Inhibits cell growth in vitro. {ECO:0000269|PubMed:11481438}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.302
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.0651
• hipred: N
• hipred_score: 0.153
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.785

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scgb3a1

Gene ontology

• Biological process: regulation of signaling receptor activity;negative regulation of cell growth;regulation of cell population proliferation;positive regulation of myoblast fusion
• Cellular component: extracellular space;extracellular exosome
• Molecular function: cytokine activity