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

Summary

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: mouse all
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Genomic context

Location:: 14q23.3

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (64746283..64879907, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (58954121..59087910, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (65213001..65346625, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

[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].
[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].
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH36893 (e-PCR)
- UniSTS:84759

GDB:434768 (e-PCR)
- UniSTS:157209

D14S830 (e-PCR)
- UniSTS:59683

D8S2279 (e-PCR)
- UniSTS:473907

RH68567 (e-PCR)
- UniSTS:36667

D14S1306 (e-PCR)
- UniSTS:39778

u00828 (e-PCR)
- UniSTS:66950

RH91150 (e-PCR)
- UniSTS:92565

RH44911 (e-PCR)
- UniSTS:77753

D14S817E (e-PCR)
- UniSTS:153792

RH91388 (e-PCR)
- UniSTS:84693

D14S1213 (e-PCR)
- UniSTS:30435

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
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
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

NG_016202.2 RefSeqGene

Range

4986..138610

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GenBank, FASTA, Sequence Viewer (Graphics), LRG_1130

mRNA and Protein(s)

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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

64746283..64879907 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047431724.1 → XP_047287680.1 spectrin beta chain, erythrocytic isoform X1
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
XM_047431725.1 → XP_047287681.1 spectrin beta chain, erythrocytic isoform X1
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

NC_060938.1 Alternate T2T-CHM13v2.0

Range

58954121..59087910 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054376644.1 → XP_054232619.1 spectrin beta chain, erythrocytic isoform X1
XM_054376641.1 → XP_054232616.1 spectrin beta chain, erythrocytic isoform X1
XM_054376643.1 → XP_054232618.1 spectrin beta chain, erythrocytic isoform X1
XM_054376642.1 → XP_054232617.1 spectrin beta chain, erythrocytic isoform X1
XM_054376645.1 → XP_054232620.1 spectrin beta chain, erythrocytic isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_000347.5: Suppressed sequence

Description

NM_000347.5: This RefSeq was removed because currently there is insufficient support for the transcript.