SBNO2

strawberry notch homolog 2

Basic information

Region (hg38): 19:1107636-1174268

Previous symbols: [ "KIAA0963" ]

Links

ENSG00000064932 ∙ NCBI:22904 ∙ OMIM:615729 ∙ HGNC:29158 ∙ Uniprot:Q9Y2G9 ∙ 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 SBNO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBNO2 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				6	1	7
missense			112	3		115
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	113	10	1

Variants in SBNO2

This is a list of pathogenic ClinVar variants found in the SBNO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1108230-G-C		not specified	Uncertain significance (May 17, 2023)
19-1108248-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-1108264-T-A		not specified	Uncertain significance (Feb 17, 2023)
19-1108312-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-1108339-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-1108347-G-C		not specified	Uncertain significance (Nov 12, 2021)
19-1108380-T-A		not specified	Uncertain significance (Nov 06, 2023)
19-1108419-G-T		not specified	Uncertain significance (Oct 29, 2021)
19-1108443-G-T		not specified	Uncertain significance (Jan 07, 2022)
19-1108459-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-1108464-G-C		not specified	Uncertain significance (Nov 01, 2022)
19-1108465-G-A		not specified	Uncertain significance (Aug 02, 2023)
19-1108467-C-A		not specified	Uncertain significance (May 13, 2022)
19-1108467-C-T		not specified	Uncertain significance (May 04, 2023)
19-1108470-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-1108479-G-C		not specified	Uncertain significance (Jun 10, 2024)
19-1108492-G-A		not specified	Uncertain significance (Apr 24, 2024)
19-1108497-G-C		not specified	Uncertain significance (Dec 27, 2023)
19-1108501-A-C		not specified	Uncertain significance (Jun 27, 2023)
19-1108509-G-C		not specified	Uncertain significance (Apr 01, 2024)
19-1108530-G-A		not specified	Uncertain significance (Jan 12, 2024)
19-1108569-C-T		not specified	Uncertain significance (May 18, 2023)
19-1108618-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-1108796-T-C		not specified	Uncertain significance (Apr 26, 2024)
19-1108802-G-C		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SBNO2	protein_coding	protein_coding	ENST00000361757	31	66647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00707	0.993	124586	0	80	124666	0.000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	614	810	0.758	0.0000588	8590
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00412	0.00396
Ashkenazi Jewish	0.000107	0.0000993
East Asian	0.0000571	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000114	0.000106
Middle Eastern	0.0000571	0.0000556
South Asian	0.00	0.00
Other	0.000344	0.000330

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.575
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.599

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sbno2
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; immune system phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: sbno2a
• Affected structure: neuroepithelial cell
• Phenotype tag: abnormal
• Phenotype quality: dislocated

Gene ontology

• 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;regulation of inflammatory response;bone trabecula morphogenesis;cellular response to lipopolysaccharide;cellular response to interleukin-11;cellular response to interleukin-6;osteoclast fusion;cellular response to leukemia inhibitory factor
• Cellular component: cellular_component;nucleus