SCGB2B2

secretoglobin family 2B member 2, the group of Secretoglobins

Basic information

Region (hg38): 19:34590644-34677159

Previous symbols: [ "SCGBL" ]

Links

ENSG00000205209 ∙ NCBI:284402 ∙ OMIM:615063 ∙ HGNC:27616 ∙ Uniprot:Q4G0G5 ∙ 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 SCGB2B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCGB2B2 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in SCGB2B2

This is a list of pathogenic ClinVar variants found in the SCGB2B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34593562-G-T		not specified	Uncertain significance (Dec 20, 2023)
19-34593578-C-T		not specified	Uncertain significance (Jun 28, 2022)
19-34594230-T-C		not specified	Uncertain significance (Mar 01, 2023)
19-34594236-T-C		not specified	Uncertain significance (Jan 04, 2024)
19-34594237-T-C		not specified	Uncertain significance (Aug 19, 2021)
19-34594260-G-T		not specified	Uncertain significance (Feb 17, 2022)
19-34594275-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-34594337-A-T		not specified	Uncertain significance (Nov 20, 2024)
19-34594339-C-T		not specified	Uncertain significance (Nov 22, 2024)
19-34594517-C-A		not specified	Uncertain significance (Dec 28, 2022)
19-34594527-C-G		not specified	Uncertain significance (Mar 14, 2023)
19-34594559-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCGB2B2	protein_coding	protein_coding	ENST00000601241	3	82371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00106	0.391	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.233	59	54.2	1.09	0.00000295	623
Missense in Polyphen		15	13.162	1.1397		167
Synonymous	0.642	20	24.0	0.833	0.00000153	192
Loss of Function	-0.311	4	3.38	1.18	1.44e-7	39

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.416

Essentials

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

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular region