SCGB2A2

secretoglobin family 2A member 2, the group of Secretoglobins

Basic information

Region (hg38): 11:62270158-62273160

Previous symbols: [ "MGB1", "PSBP1" ]

Links

ENSG00000110484 ∙ NCBI:4250 ∙ OMIM:605562 ∙ HGNC:7050 ∙ Uniprot:Q13296 ∙ 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 SCGB2A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB2A2 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in SCGB2A2

This is a list of pathogenic ClinVar variants found in the SCGB2A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62270231-G-T		not specified	Uncertain significance (Aug 05, 2024)
11-62270244-G-A		not specified	Uncertain significance (Feb 25, 2025)
11-62270908-T-A		not specified	Uncertain significance (Sep 27, 2024)
11-62270976-G-A		not specified	Uncertain significance (Feb 08, 2025)
11-62270985-G-A		not specified	Uncertain significance (Aug 20, 2024)
11-62270986-C-T		not specified	Uncertain significance (Dec 14, 2023)
11-62271034-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-62271058-A-G		not specified	Likely benign (Oct 26, 2022)
11-62271063-T-C		not specified	Likely benign (Dec 03, 2021)
11-62272964-T-C		not specified	Uncertain significance (Oct 12, 2021)
11-62272966-T-C		not specified	Uncertain significance (Jan 27, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB2A2	protein_coding	protein_coding	ENST00000227918	3	3002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000175	0.280	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.234	44	48.6	0.906	0.00000241	619
Missense in Polyphen		10	12.1	0.82643		163
Synonymous	0.0403	20	20.2	0.989	0.00000125	161
Loss of Function	-0.530	5	3.87	1.29	1.63e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.440
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0152
• hipred: N
• hipred_score: 0.112
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.202

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scgb2a2

Gene ontology

• Biological process: biological_process;androgen receptor signaling pathway
• Cellular component: cellular_component;extracellular region;extracellular space
• Molecular function: molecular_function;protein binding