SBNO2

protein-coding

strawberry notch homolog 2

Gene summary

Predicted to enable chromatin DNA binding activity and histone binding activity. Involved in several processes, including cellular response to interleukin-6; macrophage activation involved in immune response; and negative regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA0963

MANE transcript

NM_014963.3

Inheritance

—

ClinVar variants

U:293B:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr19:1,107,637-1,174,268

External References & Databases

Ensembl (ENSG00000064932)

Transcript & Mutation Effects

hg38 • Region Span ~66.6 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 SBNO2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 295

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014963.3. 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			2 clinvar	10 clinvar		12
missense			282 clinvar	17 clinvar		299
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	293	27	0	320

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014963.3	RefSeq	NP_055778.2	31	MANE Select
ENST00000361757.8	Ensembl	ENSP00000354733.2	31	MANE Select
NM_001100122.2	RefSeq	NP_001093592.1	29	Standard
ENST00000438103.6	Ensembl	ENSP00000400762.1	29	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
sbno2a	Danio rerio	Structure: neuroepithelial cell Quality: dislocated abnormal

Gene / Model

Organism

Observed Phenotype

sbno2a

Danio rerio

Structure: neuroepithelial cell

Quality: dislocated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

macrophage activation involved in immune response
bone mineralization
osteoclast differentiation
negative regulation of transcription, DNA-templated
positive regulation of transcription by RNA polymerase II

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361757
Coding exons: 31
Length: 66647
Individuals with no LoFs: 124586
Homozygous LoFs: 0
Heterozygous LoFs: 80
Defined: 124666
p: 0.000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.44	614	810	0.758	0.0000588	8590
Missense (PolyPhen)		128	275.64	0.46437		2613
Synonymous	-4.37	480	373	1.29	0.0000306	2720
Loss of Function	5.18	16	58.9	0.272	0.00000275	683

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0040	0.0039	notable
Latino/Admixed American	0.000090	0.000087	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.000057	0.000056	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0	0.0	absent
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional coregulator, that can have both coactivator and corepressor functions. Inhibits the DCSTAMP- repressive activity of TAL1, hence enhancing the access of the transcription factor MITF to the DC-STAMP promoter in osteoclast. Plays a role in bone homeostasis; required as a positive regulator in TNFSF11//RANKL-mediated osteoclast fusion via a DCSTAMP- dependent pathway. May also be required in the regulation of osteoblast differentiation (By similarity). Involved in the transcriptional corepression of NF-kappaB in macrophages (PubMed:18025162). Plays a role as a regulator in the proinflammatory cascade (PubMed:18025162). {ECO:0000250|UniProtKB:Q7TNB8, ECO:0000269|PubMed:18025162}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.0523
RVIS EVS: -2.27
RVIS percentile EVS: 1.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.599

Gene Damage Prediction

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