SBNO1

strawberry notch homolog 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 12:123289108-123364847

Links

ENSG00000139697 ∙ NCBI:55206 ∙ OMIM:614274 ∙ HGNC:22973 ∙ Uniprot:A3KN83 ∙ 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 SBNO1 gene.

• Inborn genetic diseases (27 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBNO1 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				3	3	6
missense			27	1	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding						0
Total	0	0	27	4	5

Variants in SBNO1

This is a list of pathogenic ClinVar variants found in the SBNO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-123298083-G-A			Benign (Jun 18, 2018)
12-123309316-T-C			Benign (Nov 15, 2018)
12-123309502-A-G		not specified	Uncertain significance (Dec 14, 2023)
12-123309546-A-C		not specified	Uncertain significance (May 17, 2023)
12-123309550-C-T		not specified	Uncertain significance (Jun 22, 2022)
12-123311062-G-A			Likely benign (Aug 15, 2018)
12-123311112-T-C		not specified	Uncertain significance (Mar 07, 2024)
12-123313638-G-T		not specified	Uncertain significance (Jul 11, 2023)
12-123319961-A-G		not specified	Uncertain significance (Jan 23, 2024)
12-123319997-T-C		not specified	Uncertain significance (Oct 12, 2022)
12-123320000-T-C		not specified	Uncertain significance (Dec 03, 2021)
12-123320488-G-C		not specified	Uncertain significance (Sep 29, 2023)
12-123320586-T-C		not specified	Uncertain significance (Aug 14, 2023)
12-123320714-G-A			Benign (Dec 31, 2019)
12-123320738-A-T		not specified	Uncertain significance (Jun 09, 2022)
12-123321537-T-C			Likely benign (Dec 31, 2019)
12-123321636-T-C		not specified	Uncertain significance (Feb 22, 2023)
12-123321676-T-A		not specified	Uncertain significance (Mar 14, 2023)
12-123321694-C-T		not specified	Uncertain significance (Dec 12, 2023)
12-123321736-C-T			Benign (Jan 01, 2019)
12-123323733-T-C		not specified	Uncertain significance (Jan 29, 2024)
12-123326191-C-G		not specified	Uncertain significance (Jun 12, 2023)
12-123326316-G-A		not specified	Uncertain significance (Mar 24, 2023)
12-123326331-C-T		not specified	Uncertain significance (Apr 11, 2023)
12-123327582-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SBNO1	protein_coding	protein_coding	ENST00000420886	31	75735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.89e-12	117377	0	1	117378	0.00000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.36	485	743	0.653	0.0000387	9109
Missense in Polyphen		92	271.27	0.33915		3286
Synonymous	-1.46	294	264	1.11	0.0000146	2655
Loss of Function	7.98	2	78.1	0.0256	0.00000433	952

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000175	0.000175

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.0181
• rvis_EVS: -0.82
• rvis_percentile_EVS: 12.01

Haploinsufficiency Scores

• pHI: 0.759
• hipred: Y
• hipred_score: 0.673
• ghis: 0.622

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sbno1

Zebrafish Information Network

• Gene name: sbno1
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: broken

Gene ontology

• Biological process: regulation of transcription, DNA-templated;biological_process
• Cellular component: cellular_component;nucleus
• Molecular function: molecular_function