Menu
GeneBe

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

ENSG00000189091NCBI:23450OMIM:605592HGNC:10770Uniprot:Q15393AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3B3 gene.

  • Inborn genetic diseases (15 variants)
  • not provided (2 variants)

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
16
clinvar
16
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 17 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)3160831
16-70532489-A-G not specified Uncertain significance (Sep 16, 2021)3160832
16-70532519-C-T not specified Uncertain significance (Apr 17, 2023)2537282
16-70535361-A-G not specified Uncertain significance (Dec 03, 2021)2264107
16-70535362-T-A Uncertain significance (Jul 22, 2021)1677388
16-70535362-T-G not specified Uncertain significance (Aug 15, 2023)2618692
16-70539143-G-A not specified Uncertain significance (Dec 31, 2023)3160825
16-70541700-G-T not specified Uncertain significance (Jan 31, 2024)3160826
16-70548427-C-T not specified Uncertain significance (Oct 03, 2023)3160827
16-70548430-C-T Uncertain significance (Jun 23, 2023)2572290
16-70548437-T-C not specified Uncertain significance (May 31, 2023)2554358
16-70554544-G-T Malignant tumor of prostate Uncertain significance (-)161663
16-70556257-C-G not specified Uncertain significance (Jun 24, 2022)2296602
16-70556991-G-A not specified Uncertain significance (Mar 07, 2023)2494890
16-70560588-G-C not specified Uncertain significance (Jan 24, 2024)3160828
16-70561649-G-A not specified Uncertain significance (Jun 03, 2022)2293817
16-70563975-C-A not specified Uncertain significance (Feb 06, 2023)2467970
16-70563992-C-T not specified Uncertain significance (Mar 31, 2023)2524890
16-70564009-A-C not specified Uncertain significance (Oct 06, 2021)2376828
16-70565143-C-A not specified Uncertain significance (Dec 02, 2021)2241881
16-70567444-C-T not specified Uncertain significance (May 15, 2023)2538073
16-70568286-A-G not specified Uncertain significance (Feb 05, 2024)3160829
16-70568377-G-A not specified Uncertain significance (Jun 23, 2023)2602083
16-70568452-A-G not specified Uncertain significance (Mar 07, 2023)2495333
16-70569052-C-T not specified Uncertain significance (Apr 18, 2023)2508632

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SF3B3protein_codingprotein_codingENST00000302516 2551130
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.005.81e-71257350101257450.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense5.183086920.4450.00003827934
Missense in Polyphen62264.090.234772991
Synonymous-0.9262802611.070.00001372467
Loss of Function6.87666.40.09040.00000410710

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.00009920.0000992
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00006170.0000615
Middle Eastern0.000.00
South Asian0.000.00
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sf3b3
Phenotype

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