SCGB2A1

secretoglobin family 2A member 1, the group of Secretoglobins

Basic information

Region (hg38): 11:62208673-62213943

Previous symbols: [ "MGB2" ]

Links

ENSG00000124939 ∙ NCBI:4246 ∙ OMIM:604398 ∙ HGNC:7051 ∙ Uniprot:O75556 ∙ 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 SCGB2A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB2A1 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in SCGB2A1

This is a list of pathogenic ClinVar variants found in the SCGB2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62208738-C-G		not specified	Uncertain significance (Jun 05, 2023)
11-62208747-G-A		not specified	Likely benign (Jun 26, 2024)
11-62208759-G-T		not specified	Uncertain significance (Nov 28, 2023)
11-62208772-T-C		not specified	Uncertain significance (Apr 28, 2022)
11-62208780-T-C		not specified	Uncertain significance (Nov 07, 2022)
11-62210458-A-G		not specified	Uncertain significance (Feb 12, 2024)
11-62210487-G-A		not specified	Uncertain significance (Dec 28, 2022)
11-62210500-A-T		not specified	Uncertain significance (May 23, 2023)
11-62210530-C-A		not specified	Uncertain significance (Feb 12, 2025)
11-62210533-T-C		not specified	Uncertain significance (Apr 15, 2024)
11-62210536-G-A		not specified	Uncertain significance (Jun 10, 2024)
11-62210599-T-C		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB2A1	protein_coding	protein_coding	ENST00000244930	3	5269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.232	0.655	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.173	48	51.5	0.932	0.00000248	630
Missense in Polyphen		2	4.3233	0.46261		59
Synonymous	-0.0756	20	19.6	1.02	0.00000120	159
Loss of Function	1.14	1	3.19	0.314	1.33e-7	43

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind androgens and other steroids, may also bind estramustine, a chemotherapeutic agent used for prostate cancer. May be under transcriptional regulation of steroid hormones.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.535
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.275
• hipred: N
• hipred_score: 0.112
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scgb2a2

Gene ontology

• Biological process: androgen receptor signaling pathway
• Cellular component: extracellular space
• Molecular function: protein heterodimerization activity