SF3B3

splicing factor 3b subunit 3, the group of SF3b complex|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 16:70523790-70577670

Links

ENSG00000189091 ∙ NCBI:23450 ∙ OMIM:605592 ∙ HGNC:10770 ∙ Uniprot:Q15393 ∙ 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 SF3B3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3B3 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						0
missense			24			24
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in SF3B3

This is a list of pathogenic ClinVar variants found in the SF3B3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-70529158-A-G		not specified	Uncertain significance (Jan 03, 2024)
16-70532489-A-G		not specified	Uncertain significance (Sep 16, 2021)
16-70532519-C-T		not specified	Uncertain significance (Apr 17, 2023)
16-70535361-A-G		not specified	Uncertain significance (Dec 03, 2021)
16-70535362-T-A			Uncertain significance (Jul 22, 2021)
16-70535362-T-G		not specified	Uncertain significance (Aug 15, 2023)
16-70539143-G-A		not specified	Uncertain significance (Dec 31, 2023)
16-70541700-G-T		not specified	Uncertain significance (Jan 31, 2024)
16-70548427-C-T		not specified	Uncertain significance (Oct 03, 2023)
16-70548430-C-T			Uncertain significance (Jun 23, 2023)
16-70548437-T-C		not specified	Uncertain significance (May 31, 2023)
16-70554544-G-T		Malignant tumor of prostate	Uncertain significance (-)
16-70556257-C-G		not specified	Uncertain significance (Jun 24, 2022)
16-70556991-G-A		not specified	Uncertain significance (Mar 07, 2023)
16-70560588-G-C		not specified	Uncertain significance (Jan 24, 2024)
16-70561649-G-A		not specified	Uncertain significance (Jun 03, 2022)
16-70563975-C-A		not specified	Uncertain significance (Feb 06, 2023)
16-70563992-C-T		not specified	Uncertain significance (Mar 31, 2023)
16-70564009-A-C		not specified	Uncertain significance (Oct 06, 2021)
16-70565143-C-A		not specified	Uncertain significance (Dec 02, 2021)
16-70567444-C-T		not specified	Uncertain significance (May 15, 2023)
16-70568286-A-G		not specified	Uncertain significance (Feb 05, 2024)
16-70568377-G-A		not specified	Uncertain significance (Jun 23, 2023)
16-70568452-A-G		not specified	Uncertain significance (Mar 07, 2023)
16-70569052-C-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SF3B3	protein_coding	protein_coding	ENST00000302516	25	51130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.81e-7	125735	0	10	125745	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.18	308	692	0.445	0.0000382	7934
Missense in Polyphen		62	264.09	0.23477		2991
Synonymous	-0.926	280	261	1.07	0.0000137	2467
Loss of Function	6.87	6	66.4	0.0904	0.00000410	710

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
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, a constituent of the spliceosome (PubMed:10490618, PubMed:10882114, PubMed:27720643, PubMed:28781166). 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:10490618, ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643, ECO:0000269|PubMed:28781166}.
• 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: 0.203

Intolerance Scores

• loftool: 0.274
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.04

Haploinsufficiency Scores

• pHI: 0.630
• hipred: Y
• hipred_score: 0.746
• ghis: 0.654

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sf3b3

Gene ontology

• Biological process: RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;negative regulation of protein catabolic process
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U12-type spliceosomal complex;nucleolus;small nuclear ribonucleoprotein complex;U2-type precatalytic spliceosome;catalytic step 2 spliceosome
• Molecular function: nucleic acid binding;protein binding;protein-containing complex binding