SPTBN4 spectrin beta, non-erythrocytic 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPTBN4provided by HGNC
Official Full Name: spectrin beta, non-erythrocytic 4provided by HGNC
Primary source: HGNC:HGNC:14896
See related: Ensembl:ENSG00000160460 MIM:606214; AllianceGenome:HGNC:14896
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: QV; CMND; SPNB4; NEDHND; SPTBN3
Summary: Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. This gene is one member of a family of beta-spectrin genes. The encoded protein localizes to the nuclear matrix, PML nuclear bodies, and cytoplasmic vesicles. A highly similar gene in the mouse is required for localization of specific membrane proteins in polarized regions of neurons. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 4.1), testis (RPKM 0.9) and 9 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.2

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (40467001..40576464)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (43287653..43397080)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (40972908..41082370)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Spectrin-Based Regulation of Cardiac Fibroblast Cell-Cell Communication.
Title: Spectrin-Based Regulation of Cardiac Fibroblast Cell-Cell Communication.
Novel bi-allelic variants expand the SPTBN4-related genetic and phenotypic spectrum.
Title: Novel bi-allelic variants expand the SPTBN4-related genetic and phenotypic spectrum.
betaIII spectrin controls the planarity of Purkinje cell dendrites by modulating perpendicular axon-dendrite interactions.
Title: βIII spectrin controls the planarity of Purkinje cell dendrites by modulating perpendicular axon-dendrite interactions.
bi-allelic pathogenic SPTBN4 variants (three homozygous and two compound heterozygous) that cause a severe neurological syndrome that includes congenital hypotonia, intellectual disability, and motor axonal and auditory neuropathy, are reported.
Title: βIV Spectrinopathies Cause Profound Intellectual Disability, Congenital Hypotonia, and Motor Axonal Neuropathy.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with hypotonia, neuropathy, and deafness MedGen: C4479603 OMIM: 617519 GeneReviews: SPTBN4 Disorder	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
retropepsin	gag-pol	A number of focal adhesion plaque proteins are specifically cleaved by HIV-1 protease, including fimbrin, focal adhesion plaque kinase (FAK), talin, and, to a lesser extent, filamin, spectrin and fibronectin	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A009D36 (e-PCR)
- UniSTS:3860

SHGC-33106 (e-PCR)
- UniSTS:40483

G67801 (e-PCR)
- UniSTS:225577

RH16416 (e-PCR)
- UniSTS:25928

RH46045 (e-PCR)
- UniSTS:28497

Spnb4 (e-PCR), detects polymorphism
- UniSTS:498516

SPTBN4_2491 (e-PCR)
- UniSTS:281029

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin binding	ISS Inferred from Sequence or Structural Similarity more info
enables actin filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables ankyrin binding	IDA Inferred from Direct Assay more info	PubMed
enables cytoskeletal protein-membrane anchor activity	TAS Traceable Author Statement more info	PubMed
enables phosphatase binding	IPI Inferred from Physical Interaction more info	PubMed
enables phospholipid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables spectrin binding	ISS Inferred from Sequence or Structural Similarity more info
enables structural constituent of cytoskeleton	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in actin filament capping	IEA Inferred from Electronic Annotation more info
involved_in adult walking behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in axonogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cardiac conduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in central nervous system projection neuron axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in central nervous system projection neuron axonogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in clustering of voltage-gated sodium channels	ISS Inferred from Sequence or Structural Similarity more info
involved_in fertilization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of heart rate	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuromuscular junction development	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in protein localization to plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein-containing complex assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of sodium ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in sensory perception of sound	ISS Inferred from Sequence or Structural Similarity more info
involved_in transmission of nerve impulse	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle-mediated transport	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in PML body	IDA Inferred from Direct Assay more info	PubMed
located_in actin filament	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with adherens junction	ISS Inferred from Sequence or Structural Similarity more info
located_in axon hillock	ISS Inferred from Sequence or Structural Similarity more info
located_in axon initial segment	ISS Inferred from Sequence or Structural Similarity more info
located_in cell body fiber	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cell junction	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cell projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cortical actin cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in intercalated disc	IEA Inferred from Electronic Annotation more info
located_in juxtaparanode region of axon	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in node of Ranvier	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear matrix	IDA Inferred from Direct Assay more info	PubMed
located_in paranode region of axon	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
part_of spectrin	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: spectrin beta chain, non-erythrocytic 4

Names: beta-IV spectrin; spectrin beta chain, brain 3; spectrin, non-erythroid beta chain 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029905.2 RefSeqGene

Range

5002..114465

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_020971.3 → NP_066022.2 spectrin beta chain, non-erythrocytic 4 isoform sigma1

See identical proteins and their annotated locations for NP_066022.2

Status: REVIEWED

Description

Transcript Variant: This variant (sigma1) represents the longer transcript and encodes the longer isoform (sigma1), also known as the 289 kDa isoform.

Source sequence(s)

AB046862, AC020929, AF311855, AI962525

Consensus CDS

CCDS12559.1

UniProtKB/Swiss-Prot

E9PGQ5, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0

UniProtKB/TrEMBL

C9JY79, E9PDB1, Q71S07

Related

ENSP00000469242.1, ENST00000598249.6

Conserved Domains (7) summary

smart00150
Location:1091 → 1195

SPEC; Spectrin repeats

cd00014
Location:181 → 284

CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...

cd00176
Location:1516 → 1727

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

cd10571
Location:2421 → 2525

PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain

pfam00169
Location:2419 → 2527

PH; PH domain

pfam00435
Location:1834 → 1933

Spectrin; Spectrin repeat

cl02488
Location:311 → 419

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
NM_025213.3 → NP_079489.2 spectrin beta chain, non-erythrocytic 4 isoform sigma5

Status: REVIEWED

Description

Transcript Variant: This variant (sigma5) contains a distinct 5' and 3' UTR and lacks an in-frame portion of the 5' and 3' coding region, compared to variant sigma1. The resulting isoform (sigma5), also known as the 77 kDa isoform, has distinct and shorter N- and C-termini when compared to isoform sigma1.

Source sequence(s)

AC020929, AF311856, DA514440

Consensus CDS

CCDS42569.1

UniProtKB/Swiss-Prot

Q9H254

Related

ENSP00000375877.1, ENST00000392023.1

Conserved Domains (1) summary

cd00176
Location:192 → 403

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

40467001..40576464

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017027051.2 → XP_016882540.1 spectrin beta chain, non-erythrocytic 4 isoform X3

UniProtKB/TrEMBL

M0QZQ3

Related

ENSP00000470693.1, ENST00000595535.5
XM_017027052.2 → XP_016882541.1 spectrin beta chain, non-erythrocytic 4 isoform X4
XM_017027049.2 → XP_016882538.1 spectrin beta chain, non-erythrocytic 4 isoform X1

UniProtKB/Swiss-Prot

E9PGQ5, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0

UniProtKB/TrEMBL

C9JY79, E9PDB1, Q71S07

Conserved Domains (7) summary

smart00150
Location:1091 → 1195

SPEC; Spectrin repeats

cd00014
Location:181 → 284

CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...

cd00176
Location:1516 → 1727

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

cd10571
Location:2421 → 2525

PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain

pfam00169
Location:2419 → 2527

PH; PH domain

pfam00435
Location:1834 → 1933

Spectrin; Spectrin repeat

cl02488
Location:311 → 419

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
XM_017027050.2 → XP_016882539.1 spectrin beta chain, non-erythrocytic 4 isoform X2

UniProtKB/TrEMBL

C9JY79, E9PDB1, Q71S07

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

43287653..43397080

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321577.1 → XP_054177552.1 spectrin beta chain, non-erythrocytic 4 isoform X3
XM_054321578.1 → XP_054177553.1 spectrin beta chain, non-erythrocytic 4 isoform X4
XM_054321575.1 → XP_054177550.1 spectrin beta chain, non-erythrocytic 4 isoform X1

UniProtKB/Swiss-Prot

E9PGQ5, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0
XM_054321576.1 → XP_054177551.1 spectrin beta chain, non-erythrocytic 4 isoform X2