SF3B2

splicing factor 3b subunit 2, the group of Armadillo like helical domain containing|SF3b complex

Basic information

Region (hg38): 11:66050729-66069308

Links

ENSG00000087365 ∙ NCBI:10992 ∙ OMIM:605591 ∙ HGNC:10769 ∙ Uniprot:Q13435 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Craniofacial microsomia 1	AD	Cardiovascular	Individuals have been described with congenital structural cardiovascular anomalies, and surveillance may allow early identification and management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	34344887

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3B2 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				1	1	2
missense			32	5		37
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding						0
Total	0	0	34	6	1

Variants in SF3B2

This is a list of pathogenic ClinVar variants found in the SF3B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66052385-A-T		Craniofacial microsomia 1	Pathogenic (Jul 13, 2023)
11-66052460-G-T			Benign/Likely benign (May 01, 2024)
11-66053023-G-T		SF3B2-related disorder	Likely benign (May 14, 2024)
11-66053037-T-G		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
11-66055118-C-G		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
11-66055135-G-C			Likely benign (Jul 01, 2023)
11-66055140-C-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
11-66055218-G-C			Uncertain significance (Mar 14, 2022)
11-66055269-A-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
11-66055572-A-G		Inborn genetic diseases	Uncertain significance (Apr 04, 2023)
11-66055571-G-GAGC			Uncertain significance (Jan 01, 2024)
11-66056919-G-C		Inborn genetic diseases	Uncertain significance (Mar 27, 2023)
11-66056952-C-T		Craniofacial microsomia 1	Pathogenic (Jul 17, 2023)
11-66057301-A-G		Inborn genetic diseases	Likely benign (Jan 31, 2024)
11-66057317-G-C		Inborn genetic diseases	Uncertain significance (Jun 19, 2024)
11-66057322-C-T		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
11-66057328-C-G		Inborn genetic diseases	Likely benign (Dec 13, 2023)
11-66057331-C-T		Inborn genetic diseases	Uncertain significance (Nov 03, 2023)
11-66057350-C-T		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
11-66057358-G-A		Inborn genetic diseases	Uncertain significance (Mar 28, 2024)
11-66057366-G-T		SF3B2-related disorder	Uncertain significance (Jul 18, 2023)
11-66058124-G-T		Inborn genetic diseases	Uncertain significance (Dec 14, 2021)
11-66058344-C-T		Inborn genetic diseases	Likely benign (Feb 28, 2023)
11-66058836-C-T		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
11-66058911-C-T		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SF3B2	protein_coding	protein_coding	ENST00000322535	22	18580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000800	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.68	291	530	0.550	0.0000309	5831
Missense in Polyphen		75	179.34	0.4182		1931
Synonymous	-0.411	203	196	1.04	0.0000107	1760
Loss of Function	6.00	6	53.2	0.113	0.00000305	590

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000685	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000143	0.000139
European (Non-Finnish)	0.000274	0.000246
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077). {ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.0547
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.809
• ghis: 0.634

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sf3b2

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mRNA processing;RNA splicing;viral process
• Cellular component: nucleoplasm;spliceosomal complex;U2 snRNP;U12-type spliceosomal complex;nuclear speck;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding