BSPRY

protein-coding

B-box and SPRY domain containing

Gene summary

Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017688.3

Inheritance

—

ClinVar variants

U:88B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr9:113,349,541-113,371,233

External References & Databases

Ensembl (ENSG00000119411)

Transcript & Mutation Effects

hg38 • Region Span ~21.7 kb

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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 BSPRY variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017688.3. 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			1 clinvar	1 clinvar		2
missense			86 clinvar	4 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	88	5	0	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017688.3	RefSeq	NP_060158.2	6	MANE Select
ENST00000374183.5	Ensembl	ENSP00000363298.4	6	MANE Select
NM_001317943.2	RefSeq	NP_001304872.1	6	Standard
NM_001317944.2	RefSeq	NP_001304873.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

calcium ion transport
cellular response to leukemia inhibitory factor

Molecular Function

zinc ion binding

Cellular Component

membrane
cell leading edge
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374183
Coding exons: 6
Length: 21693
Individuals with no LoFs: 124821
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 124859
p: 0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.129	209	214	0.975	0.0000133	2568
Missense (PolyPhen)		63	70.09	0.89885		862
Synonymous	0.565	85	91.9	0.925	0.00000594	830
Loss of Function	0.990	11	15.2	0.726	7.13e-7	180

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00067	0.00064	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate epithelial calcium transport by inhibiting TRPV5 activity. {ECO:0000250}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.697
RVIS EVS: 0.22
RVIS percentile EVS: 68.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.227

Gene Damage Prediction

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