SF3B4 splicing factor 3b subunit 4

Gene info


SAP49, SF3b49, Hsh49

Previous symbol


External ID

HGNC: 10771
Entrez Gene: 10262
Ensembl: ENSG00000143368
UCSC: uc001etk.3
OMIM: 605593
UniProtKB: Q15427

Disease info

CHD Phenotype

  • Ventricular septal defect
  • Patent ductus arteriosus
  • Atrioventricular septal defect
  • Tetralogy of fallot

Extra Cardiac Phenotype

Short stature , Microcephaly , Micrognathia , Midface retrusion, Retrognathia , Conductive deafness , Low-set ears , Posteriorly rotated ears , Preauricular tags , External auditory canal atresia , Downslanting palpebral fissures , Partial-total absence of lower eyelashes , Lower lid coloboma , High nasal bridge, Cleft palate , Cleft lip, Macrostomia, Trismus , Velopharyngeal insufficiency, Laryngeal hypoplasia , Hypoplasia of the epiglottis , Hypoplastic first rib , Gastroschisis , Hirschsprung disease , Bicornuate uterus, Unilateral renal agenesis , Duplicated calyx, Hypoplastic zygomatic arch, Hypoplastic mandible, Scoliosis , Cervical vertebral abnormalities, Hip dislocation , Radioulnar synostosis , Limitation of elbow extension , Short forearms , Radial aplasia , Radial hypoplasia, Thumb aplasia/hypoplasia , Syndactyly , Clinodactyly , Triphalangeal thumbs , Missing toes , Hypoplastic toes, Toe syndactyly , Overlapping toes, Hallux valgus , Broad hallux, Clubfeet , Urticaria pigmentosa , Partial to total absence of eyelashes , Normal intelligence , Hydrocephalus , Aqueductal stenosis, Polymicrogyria, Speech delay , Premature birth

Incomplete penetrance


Variable expressivity


Animal model

Mouse study

MGI: No cardiovascular defect recorded in knockout mice


Variant info


Selected variant

The Clinvar variants presented in the below IGV track were selected based on the following criteria.

  1. Variant types are single nucleotide variant or Indel
  2. Clinical significance for the variant was assessed to be Pathogenic or Likely Pathogenic
  3. ClinVar review status for the variant is criteria provided

Download annotation file for SF3B4: BED file

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Selected References

  1. Lehalle, D., Wieczorek, D., Zechi-Ceide, R. M., Passos-Bueno, M. R., Lyonnet, S., Amiel, J., & Gordon, C. T. (2015). A review of craniofacial disorders caused by spliceosomal defects. Clinical Genetics, 88(5), 405–415. Portico. https://doi.org/10.1111/cge.12596 DOI:10.1111/cge.12596 PMID:25865758
  2. Bernier, F. P., Caluseriu, O., Ng, S., Schwartzentruber, J., Buckingham, K. J., Innes, A. M., Jabs, E. W., Innis, J. W., Schuette, J. L., Gorski, J. L., Byers, P. H., Andelfinger, G., Siu, V., Lauzon, J., Fernandez, B. A., McMillin, M., Scott, R. H., Racher, H., Majewski, J., … Parboosingh, J. S. (2012). Haploinsufficiency of SF3B4, a Component of the Pre-mRNA Spliceosomal Complex, Causes Nager Syndrome. The American Journal of Human Genetics, 90(5), 925–933. https://doi.org/10.1016/j.ajhg.2012.04.004 DOI:10.1016/j.ajhg.2012.04.004 PMID:22541558
  3. Petit, F., Escande, F., Jourdain, A. S., Porchet, N., Amiel, J., Doray, B., Delrue, M. A., Flori, E., Kim, C. A., Marlin, S., Robertson, S. P., Manouvrier-Hanu, S., & Holder-Espinasse, M. (2013). Nager syndrome: confirmation ofSF3B4haploinsufficiency as the major cause. Clinical Genetics, 86(3), 246–251. Portico. https://doi.org/10.1111/cge.12259 DOI:10.1111/cge.12259 PMID:24003905