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Intellectual disability

Gene: SF3B1

Amber List (moderate evidence)
SF3B1 (splicing factor 3b subunit 1)
EnsemblGeneIds (GRCh38): ENSG00000115524
EnsemblGeneIds (GRCh37): ENSG00000115524
OMIM: 605590, Gene2Phenotype
SF3B1 is in 5 panels

2 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are now numerous individuals reported with monoallelic (mostly de novo) variants in SF3B1, presenting with syndromic ID/GDD. Based on available evidence, this gene can be promoted to Green at the next update.
Created: 17 Jun 2026, 5:21 p.m. | Last Modified: 17 Jun 2026, 5:21 p.m.
Panel Version: 10.23
As reviewed by Karen Stals, Uguen et al. (PMID: 41577671, 2026) reported 26 patients with heterozygous SF3B1 variants. Most of them were confirmed to be de novo, with 3 cases where variant was inherited from a parent (2 parents with learning difficulties, and 1 asymptomatic father). Seq method: Trio or Solo WES. 3 patients had VUS variants in other genes.
"Almost all (23/26) affected individuals exhibited at least one neurodevelopmental abnormality, the most frequent being language delay (21/26). Motor delay was found in 18/24 individuals. Intellectual disability (ID) was present in 9/15 individuals, some cases being too young (8/26) to assess. The severity of ID was mainly mild to moderate, only two individuals presenting with severe ID. Seizures were reported in 13 individuals, with variable ages of onset and types." Other features: hypotonia (11 patients), spastic quadriplegia (2 patients without NDD), non-specific brain MRI anomalies (4 cases), cleft palate or high-arched palate (12 patients), heart defects (8/25), postnatal short stature (6), IUGR (5), microcephaly (7/22 assessed).

De novo missense variants in the SF3B1 gene have also been identified in ASD probands (PMID: 25363768 Iossifov et al., 2014 - 2 probands with ASD, harbouring SF3B1 variants c.1078A>G, p.Ile360Val & c.890C>A, p.Pro297His) and two probands with unspecified developmental disorders, with de novo SF3B1 variants c.1108C>T, p.Pro370Ser & c.1781G>A, p.Arg594Gln (PMID: 28135719 Deciphering Developmental Disorders Study 2017).

SF3B1 is not yet associated with an NDD in OMIM, and it has not been classified in ClinGen (accessed 17th Jun 2026). The gene is Green in PanelApp Australia on 'Intellectual disability syndromic and non-syndromic' panel.
Created: 17 Jun 2026, 5:11 p.m. | Last Modified: 17 Jun 2026, 5:19 p.m.
Panel Version: 10.22

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Complex neurodevelopmental disorder, MONDO:0100038

Publications

Created: 17 Jun 2026, 5:11 p.m.
Last Modified: 17 Jun 2026, 5:19 p.m.
Panel version: 10.22

Karen Stals (Royal Devon and Exeter Hospital)

Green List (high evidence)

PMID: 41577671 report 26 individuals with a neurodevelopmental disorder and a SF3B1 heterozygous variant - loss of function (n = 9) and missense variants (n = 17) (mostly de novo), authors propose a more severe phenotype associated with missense variants
Sources: Literature
Created: 11 Jun 2026, 11:19 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Neurodevelopmental disorder; language impairment; developmental delay; seizures; dysmorphism; congenital anomalies

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 11 Jun 2026, 11:19 a.m.

Panel version: 10.18

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
Phenotypes
  • Complex neurodevelopmental disorder, MONDO:0100038
  • Neurodevelopmental disorder
  • language impairment
  • developmental delay
  • seizures
  • dysmorphism
  • congenital anomalies
Tags
Q2_26_promote_green Q2_26_NHS_review
OMIM
605590
Clinvar variants
Variants in SF3B1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Jun 2026, Gel status: 2

Added Tag, Added Tag

Ida Ertmanska (Genomics England Curator)

Tag Q2_26_promote_green tag was added to gene: SF3B1. Tag Q2_26_NHS_review tag was added to gene: SF3B1.

17 Jun 2026, Gel status: 2

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: SF3B1 were changed from Neurodevelopmental disorder; language impairment; developmental delay; seizures; dysmorphism; congenital anomalies to Complex neurodevelopmental disorder, MONDO:0100038; Neurodevelopmental disorder; language impairment; developmental delay; seizures; dysmorphism; congenital anomalies

17 Jun 2026, Gel status: 2

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: SF3B1 were set to PMID: 41577671

17 Jun 2026, Gel status: 2

Entity classified by Genomics England curator

Ida Ertmanska (Genomics England Curator)

Gene: sf3b1 has been classified as Amber List (Moderate Evidence).

11 Jun 2026, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Karen Stals (Royal Devon and Exeter Hospital)

gene: SF3B1 was added gene: SF3B1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: SF3B1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SF3B1 were set to PMID: 41577671 Phenotypes for gene: SF3B1 were set to Neurodevelopmental disorder; language impairment; developmental delay; seizures; dysmorphism; congenital anomalies Review for gene: SF3B1 was set to GREEN gene: SF3B1 was marked as current diagnostic