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Intellectual disability

Gene: SPTBN4

Amber List (moderate evidence)

SPTBN4 (spectrin beta, non-erythrocytic 4)
EnsemblGeneIds (GRCh38): ENSG00000160460
EnsemblGeneIds (GRCh37): ENSG00000160460
OMIM: 606214, Gene2Phenotype
SPTBN4 is in 8 panels

2 reviews

Arina Puzriakova (Genomics England Curator)

Review by Helen Brittain (Genomics England Clinical Team): the phenotype is characterised by marked hypotonia in infancy and developmental delay / ID. Adding as Green to the ID panel would therefore cover both of these GMS indications (as the Hypotonic Infant super panel has the ID panel as a sub-panel).
Created: 10 Nov 2020, 4:42 p.m. | Last Modified: 10 Nov 2020, 4:42 p.m.
Panel Version: 3.510
Comment on list classification: There is sufficient evidence to rate this gene Green at the next GMS panel update.

Severe-to-profound DD and/or ID reported in all but one family with a milder phenotype (at least 9 total families described with different biallelic variants in SPTBN4).
Created: 5 Oct 2020, 2:03 p.m. | Last Modified: 5 Oct 2020, 2:03 p.m.
Panel Version: 3.378

Konstantinos Varvagiannis (Other)

Green List (high evidence)

** Consider also the GeneReview on this disorder - PMID : 32672909
Created: 17 Sep 2020, 9:29 p.m. | Last Modified: 17 Sep 2020, 9:29 p.m.
Panel Version: 3.314
Biallelic pathogenic SPTBN4 variants cause Neurodevelopmental disorder with hypotonia, neuropathy, and deafness (MIM #617519).

There are several reports on the phenotype of relevant affected individuals with severe/profound DD/ID in at least 9 individuals :

- Knierim et al (2017 - PMID: 28540413) [1 affected individual]
- Anazi et al (2017 - PMID: 28940097) [1]
- Wang et al (2018 - PMID: 29861105) [6]
- Pehlivan et al (2019 - PMID: 31230720) [1]

A recent article by Häusler et al (2019 - PMID: 31857255) describes the phenotype of 2 sibs, both presenting with motor and speech delay, although the older one had reportedly 'normal' cognitive performance allowing attendance of regular school at the age of 6 years.

Features include congenital hypotonia, severe DD and ID (in most as outlined above, ID was the primary indication for testing on several occasions), poor or absent reflexes and weakness secondary to axonal motor neuropathy, feeding and respiratory difficulties, hearing and visual impairment. Seizures have been reported in at least 4 unrelated individuals (3 by Wang et al / 1 by Pehlivan et al).

Variants in most cases were nonsense/frameshift although biallelic missense variants have also been reported. Sibs in the report by Häusler et al harbored a homozygous splicing variant.

SPTBN4 encodes a member of the beta-spectrin protein family that is expressed in the brain, peripheral nervous system, pancreas, and skeletal muscle.

βIV spectrin links ankyrinG and clustered ion channels (at axon initial segments and nodes of Ranvier) to the axonal cytoskeleton. Pathogenic variants are proposed to disrupt the cytoskeletal machinery controlling proper localization of ion channels and function of axonal domains where ion channels are normally clustered in high density. Among the evidence provided : nerve biopsies from an affected individual displayed reduced nodal Na+ channels and no nodal KCNQ2 K+ channels / Loss of AnkyrinG and βIV spectrin in animal model resulted in loss of KCNQ2- and KCNQ3- subunit containing K+ channels.

Apart from the ID / epilepsy panels please consider inclusion in other relevant ones.
Sources: Literature
Created: 7 May 2020, 6:23 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Neurodevelopmental disorder with hypotonia, neuropathy, and deafness MIM#617519



Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Amber
  • Neurodevelopmental disorder with hypotonia, neuropathy, and deafness MIM#617519
Clinvar variants
Variants in SPTBN4
Panels with this gene

History Filter Activity

5 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: sptbn4 has been classified as Amber List (Moderate Evidence).

5 Oct 2020, Gel status: 0

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review tag was added to gene: SPTBN4.

7 May 2020, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: SPTBN4 was added gene: SPTBN4 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: SPTBN4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SPTBN4 were set to 28540413; 28940097; 29861105; 31230720; 31857255 Phenotypes for gene: SPTBN4 were set to Neurodevelopmental disorder with hypotonia, neuropathy, and deafness MIM#617519 Penetrance for gene: SPTBN4 were set to Complete Review for gene: SPTBN4 was set to GREEN