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SPTB spectrin beta, erythrocytic [ Homo sapiens (human) ]

Gene ID: 6710, updated on 3-Apr-2024

Summary

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Official Symbol
SPTBprovided by HGNC
Official Full Name
spectrin beta, erythrocyticprovided by HGNC
Primary source
HGNC:HGNC:11274
See related
Ensembl:ENSG00000070182 MIM:182870; AllianceGenome:HGNC:11274
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
EL3; HS2; SPH2; HSPTB1
Summary
This locus encodes a member of the spectrin gene family. Spectrin proteins, along with ankyrin, play a role in cell membrane organization and stability. The protein encoded by this locus functions in stability of erythrocyte membranes, and mutations in this gene have been associated with spherocytosis type 2, hereditary elliptocytosis, and neonatal hemolytic anemia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
Expression
Biased expression in bone marrow (RPKM 15.7), heart (RPKM 8.2) and 8 other tissues See more
Orthologs
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Genomic context

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Location:
14q23.3
Exon count:
40
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (64746283..64879907, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (58954121..59087910, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (65213001..65346625, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5839 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:65039864-65040400 Neighboring gene protein phosphatase 1 regulatory subunit 36 Neighboring gene nucleoporin 50 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65099836-65100338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65142104-65142604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65142605-65143105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65146682-65147226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65169421-65169922 Neighboring gene NANOG hESC enhancer GRCh37_chr14:65175156-65175657 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65181995-65182914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65182915-65183832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65184752-65185669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65194651-65195302 Neighboring gene pleckstrin homology and RhoGEF domain containing G3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65195956-65196607 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65202813-65203735 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65203736-65204657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:65233085-65234003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65241545-65242046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65242047-65242546 Neighboring gene microRNA 7855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65298097-65298596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:65322751-65323318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5844 Neighboring gene uncharacterized LOC105370534 Neighboring gene ribonuclease P RNA component H1, 2 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. [Analysis of the characteristics of SPTB gene variants among 16 children with Hereditary spherocytosis]. Ge Y, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2023 Mar 10. PMID 36854399
  2. [Genetic Analysis of a Chinese Pedigree with Hereditary Spherocytosis Caused by Copy Number Variation Deletion of SPTB Gene]. Chen XL, et al. Zhongguo Shi Yan Xue Ye Xue Za Zhi, 2023 Feb. PMID 36765497
  3. Whole exome sequencing identifies a novel SPTB frameshift mutation causing hereditary spherocytosis in the Chinese population. Liu XD, et al. Ann Hematol, 2022 Oct. PMID 35726106
  4. A novel SPTB mutation causes hereditary spherocytosis via loss-of-function of β-spectrin. Li S, et al. Ann Hematol, 2022 Apr. PMID 35099593
  5. The updated beta-spectrin mutations in patients with hereditary spherocytosis by targeted next-generation sequencing. Fan J, et al. J Hum Genet, 2021 Dec. PMID 34140613

See all (129) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [Analysis of the characteristics of SPTB gene variants among 16 children with Hereditary spherocytosis].
    Title: [Analysis of the characteristics of SPTB gene variants among 16 children with Hereditary spherocytosis].
  2. [Genetic Analysis of a Chinese Pedigree with Hereditary Spherocytosis Caused by Copy Number Variation Deletion of SPTB Gene].
    Title: [Genetic Analysis of a Chinese Pedigree with Hereditary Spherocytosis Caused by Copy Number Variation Deletion of SPTB Gene].
  3. Whole exome sequencing identifies a novel SPTB frameshift mutation causing hereditary spherocytosis in the Chinese population.
    Title: Whole exome sequencing identifies a novel SPTB frameshift mutation causing hereditary spherocytosis in the Chinese population.
  4. The updated beta-spectrin mutations in patients with hereditary spherocytosis by targeted next-generation sequencing.
    Title: The updated beta-spectrin mutations in patients with hereditary spherocytosis by targeted next-generation sequencing.
  5. A novel SPTB mutation causes hereditary spherocytosis via loss-of-function of beta-spectrin.
    Title: A novel SPTB mutation causes hereditary spherocytosis via loss-of-function of β-spectrin.
  6. A novel SPTB frameshift deletion causing hereditary spherocytosis identified by next-generation sequencing in a Chinese family.
    Title: A novel SPTB frameshift deletion causing hereditary spherocytosis identified by next-generation sequencing in a Chinese family.
  7. A novel essential splice site variant in SPTB in a large hereditary spherocytosis family.
    Title: A novel essential splice site variant in SPTB in a large hereditary spherocytosis family.
  8. Clinical manifestation and phenotypic analysis of novel gene mutation in 28 Chinese children with hereditary spherocytosis.
    Title: Clinical manifestation and phenotypic analysis of novel gene mutation in 28 Chinese children with hereditary spherocytosis.
  9. SPTB related spherocytosis in a three-generation family presenting with kidney failure in adulthood due to co-occurrence of UMOD disease causing variant.
    Title: SPTB related spherocytosis in a three-generation family presenting with kidney failure in adulthood due to co-occurrence of UMOD disease causing variant.
  10. A clinical and experimental study of adult hereditary spherocytosis in the Chinese population.
    Title: A clinical and experimental study of adult hereditary spherocytosis in the Chinese population.
Submit: New GeneRIF Correction See all GeneRIFs (43)

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
Elliptocytosis 3
MedGen: C1866810 OMIM: 617948 GeneReviews: Not available
Compare labs
Hereditary spherocytosis type 2
MedGen: C2674219 OMIM: 616649 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding TAS
Traceable Author Statement
more info
 PubMed 
enables actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables actin filament binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ankyrin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables structural constituent of cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
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 modification of postsynaptic actin cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in modification of postsynaptic actin cytoskeleton IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in actin cytoskeleton TAS
Traceable Author Statement
more info
 PubMed 
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 cytoplasmic side of plasma membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spectrin IEA
Inferred from Electronic Annotation
more info
  
located_in spectrin-associated cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
spectrin beta chain, erythrocytic
Names
Sp beta
beta-I spectrin
erythrocytic spectrin beta chain
membrane cytoskeletal protein
spectrin beta Tandil
spectrin beta chain, erythrocyte

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

  1. NG_016202.2 RefSeqGene

    Range
    4986..138610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1130

mRNA and Protein(s)

  1. NM_001024858.4 → NP_001020029.1  spectrin beta chain, erythrocytic isoform a

    See identical proteins and their annotated locations for NP_001020029.1

    Status: REVIEWED

    Source sequence(s)
    AB209415, AK094815, AL121774, BC010434, BX248270, CN370674, M37884
    UniProtKB/TrEMBL
    Q59FP5
    Related
    ENSP00000374372.3, ENST00000389722.7
    Conserved Domains (5) summary
    smart00150
    Location:1385 → 1475
    SPEC; Spectrin repeats
    COG5069
    Location:48 → 438
    SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
    cd00176
    Location:530 → 742
    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:2181 → 2286
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:422 → 525
    Spectrin; Spectrin repeat

  2. NM_001355436.2 → NP_001342365.1  spectrin beta chain, erythrocytic isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL121774, AL135745
    Consensus CDS
    CCDS32099.1
    UniProtKB/TrEMBL
    Q59FP5
    Related
    ENSP00000495909.1, ENST00000644917.1
    Conserved Domains (5) summary
    smart00150
    Location:1385 → 1475
    SPEC; Spectrin repeats
    COG5069
    Location:48 → 438
    SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
    cd00176
    Location:530 → 742
    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:2181 → 2286
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:422 → 525
    Spectrin; Spectrin repeat

  3. NM_001355437.2 → NP_001342366.1  spectrin beta chain, erythrocytic isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a. This variant is also referred to as muscle beta spectrin.
    Source sequence(s)
    AL121774, AL135745
    Consensus CDS
    CCDS32100.1
    UniProtKB/Swiss-Prot
    P11277, Q15510, Q15519
    UniProtKB/TrEMBL
    B2RMN7
    Related
    ENSP00000374370.4, ENST00000389720.4
    Conserved Domains (4) summary
    smart00150
    Location:1385 → 1475
    SPEC; Spectrin repeats
    COG5069
    Location:48 → 438
    SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
    cd00176
    Location:530 → 742
    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; ...
    pfam00435
    Location:422 → 525
    Spectrin; Spectrin repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    64746283..64879907 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021612.3 → XP_016877101.1  spectrin beta chain, erythrocytic isoform X1

    UniProtKB/TrEMBL
    Q59FP5
    Conserved Domains (5) summary
    smart00150
    Location:1385 → 1475
    SPEC; Spectrin repeats
    COG5069
    Location:48 → 438
    SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
    cd00176
    Location:530 → 742
    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:2181 → 2286
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:422 → 525
    Spectrin; Spectrin repeat

  2. XM_047431724.1 → XP_047287680.1  spectrin beta chain, erythrocytic isoform X1

  3. XM_024449699.2 → XP_024305467.1  spectrin beta chain, erythrocytic isoform X1

    UniProtKB/TrEMBL
    Q59FP5
    Conserved Domains (5) summary
    smart00150
    Location:1385 → 1475
    SPEC; Spectrin repeats
    COG5069
    Location:48 → 438
    SAC6; Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]
    cd00176
    Location:530 → 742
    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:2181 → 2286
    PH_beta_spectrin; Beta-spectrin pleckstrin homology (PH) domain
    pfam00435
    Location:422 → 525
    Spectrin; Spectrin repeat

  4. XM_047431725.1 → XP_047287681.1  spectrin beta chain, erythrocytic isoform X1

  5. XM_011537105.4 → XP_011535407.1  spectrin beta chain, erythrocytic isoform X2

    Conserved Domains (4) summary
    smart00033
    Location:177 → 273
    CH; Calponin homology domain
    cd00014
    Location:55 → 158
    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:530 → 742
    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; ...
    pfam00435
    Location:422 → 525
    Spectrin; Spectrin repeat

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    58954121..59087910 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376644.1 → XP_054232619.1  spectrin beta chain, erythrocytic isoform X1

  2. XM_054376641.1 → XP_054232616.1  spectrin beta chain, erythrocytic isoform X1

  3. XM_054376643.1 → XP_054232618.1  spectrin beta chain, erythrocytic isoform X1

  4. XM_054376642.1 → XP_054232617.1  spectrin beta chain, erythrocytic isoform X1

  5. XM_054376645.1 → XP_054232620.1  spectrin beta chain, erythrocytic isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_000347.5: Suppressed sequence

    Description
    NM_000347.5: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P11277.5 GenPept UniProtKB/Swiss-Prot:P11277

Gene LinkOut

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