SCGB3A1

protein-coding

secretoglobin family 3A member 1, the group of Secretoglobins

Gene summary

Predicted to enable cytokine activity. Predicted to be involved in positive regulation of myoblast fusion. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_052863.3

Inheritance

—

ClinVar variants

U:11B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr5:180,590,105-180,591,499

External References & Databases

Ensembl (ENSG00000161055)

Transcript & Mutation Effects

hg38 • Region Span ~1.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCGB3A1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052863.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			11 clinvar	5 clinvar		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	11	5	0	16

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052863.3	RefSeq	NP_443095.2	3	MANE Select
ENST00000292641.4	Ensembl	ENSP00000292641.3	3	MANE Select
ENST00000899434.1	Ensembl	ENSP00000569493.1	3	Standard
ENST00000899434.2	Ensembl	ENSP00000569493.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of signaling receptor activity
negative regulation of cell growth
regulation of cell population proliferation
positive regulation of myoblast fusion

Molecular Function

cytokine activity

Cellular Component

extracellular space
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000292641
Coding exons: 3
Length: 1438
Individuals with no LoFs: 119158
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 119161
p: 0.0000126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.322	38	44.0	0.863	0.00000194	616
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000063	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000069	0.000067	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.785

Gene Damage Prediction

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