SF3B5

protein-coding

splicing factor 3b subunit 5, the group of SF3b complex

Gene summary

Enables RNA binding activity and splicing factor binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U12-type spliceosomal complex and U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_031287.3

Inheritance

—

ClinVar variants

U:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr6:144,094,884-144,095,573

External References & Databases

Ensembl (ENSG00000169976)

Transcript & Mutation Effects

hg38 • Region Span ~0.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SF3B5 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031287.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	5	0	0	5

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031287.3	RefSeq	NP_112577.1	1	MANE Select
ENST00000367569.4	Ensembl	ENSP00000356541.2	1	MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
sf3b5	Danio rerio	Structure: trunk Quality: atrophied abnormal

Gene / Model

Organism

Observed Phenotype

sf3b5

Danio rerio

Structure: trunk

Quality: atrophied

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
mRNA Processing
Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing - Minor Pathway

Biological Process

mRNA splicing, via spliceosome

Molecular Function

RNA binding

Cellular Component

nucleus
nucleoplasm
U2 snRNP
U12-type spliceosomal complex
U2-type precatalytic spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367569
Coding exons: 1
Length: 737
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	25	48.1	0.519	0.00000224	574
Missense (PolyPhen)		7	18.795	0.37244		213
Synonymous	-0.720	23	19.0	1.21	9.84e-7	154
Loss of Function	1.53	0	2.71	0.00	1.17e-7	30

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex, a constituent of the spliceosome (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). {ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:27720643, ECO:0000269|PubMed:28781166}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

RVIS EVS: 0.1
RVIS percentile EVS: 60.96

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.977

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low