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SPTA1 spectrin alpha, erythrocytic 1 [ Homo sapiens (human) ]

Gene ID: 6708, updated on 5-Mar-2024

Summary

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Official Symbol
SPTA1provided by HGNC
Official Full Name
spectrin alpha, erythrocytic 1provided by HGNC
Primary source
HGNC:HGNC:11272
See related
Ensembl:ENSG00000163554 MIM:182860; AllianceGenome:HGNC:11272
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
EL2; HPP; HS3; SPH3; SPTA
Summary
This gene encodes a member of a family of molecular scaffold proteins that link the plasma membrane to the actin cytoskeleton and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. The encoded protein is primarily composed of 22 spectrin repeats which are involved in dimer formation. It forms a component of the erythrocyte plasma membrane. Mutations in this gene result in a variety of hereditary red blood cell disorders, including elliptocytosis-2, pyropoikilocytosis, and spherocytosis, type 3. [provided by RefSeq, Aug 2017]
Expression
Restricted expression toward bone marrow (RPKM 32.4) See more
Orthologs
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Genomic context

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Location:
1q23.1
Exon count:
52
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (158610704..158686715, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (157747803..157823815, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (158580494..158656505, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 6 subfamily P member 1 Neighboring gene olfactory receptor family 10 subfamily X member 1 Neighboring gene olfactory receptor family 10 subfamily Z member 1 Neighboring gene MPRA-validated peak429 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:158658352-158658566 Neighboring gene CRISPRi-validated cis-regulatory element chr1.9295 Neighboring gene CRISPRi-validated cis-regulatory element chr1.9296 Neighboring gene olfactory receptor family 6 subfamily K member 1 pseudogene Neighboring gene olfactory receptor family 6 subfamily K member 2

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. Hereditary elliptocytosis: A novel mutation in the SPTA1 gene and diagnosis after a stroke in paediatric patients. A two-case report. Moreno Toro N, et al. Pediatr Blood Cancer, 2023 Jul. PMID 37016817
  2. Unravelling the genetic and phenotypic heterogeneity of SPTA1 gene variants in Hereditary Elliptocytosis and Hereditary Pyropoikilocytosis patients using next-generation sequencing. Anil More T, et al. Gene, 2022 Nov 15. PMID 35961434
  3. Effects of SPTA1 Gene Variants on the Hematological Phenotype of Mexican Patients with Hereditary Spherocytosis. Herrera-Tirado IM, et al. Genet Test Mol Biomarkers, 2022 May. PMID 35638908
  4. Hereditary spherocytosis overlooked for 7 years in a pediatric patient with β-thalassemia trait and novel compound heterozygous mutations of SPTA1 gene. Chen M, et al. Hematology, 2020 Dec. PMID 33210974
  5. A Novel α-Spectrin Pathogenic Variant in Trans to α-Spectrin LELY Causing Neonatal Jaundice With Hemolytic Anemia From Hereditary Pyropoikilocytosis Coexisting With Gilbert Syndrome. Suzuki T, et al. J Pediatr Hematol Oncol, 2021 Mar 1. PMID 32287101

See all (159) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hereditary elliptocytosis: A novel mutation in the SPTA1 gene and diagnosis after a stroke in paediatric patients. A two-case report.
    Title: Hereditary elliptocytosis: A novel mutation in the SPTA1 gene and diagnosis after a stroke in paediatric patients. A two-case report.
  2. Unravelling the genetic and phenotypic heterogeneity of SPTA1 gene variants in Hereditary Elliptocytosis and Hereditary Pyropoikilocytosis patients using next-generation sequencing.
    Title: Unravelling the genetic and phenotypic heterogeneity of SPTA1 gene variants in Hereditary Elliptocytosis and Hereditary Pyropoikilocytosis patients using next-generation sequencing.
  3. Effects of SPTA1 Gene Variants on the Hematological Phenotype of Mexican Patients with Hereditary Spherocytosis.
    Title: Effects of SPTA1 Gene Variants on the Hematological Phenotype of Mexican Patients with Hereditary Spherocytosis.
  4. Complex Modes of Inheritance in Hereditary Red Blood Cell Disorders: A Case Series Study of 155 Patients.
    Title: Complex Modes of Inheritance in Hereditary Red Blood Cell Disorders: A Case Series Study of 155 Patients.
  5. 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.
  6. Novel mechanism of hereditary pyropoikilocytosis phenotype due to co-inheritance of beta globin and alpha spectrin mutations.
    Title: Novel mechanism of hereditary pyropoikilocytosis phenotype due to co-inheritance of β globin and α spectrin mutations.
  7. A Novel alpha-Spectrin Pathogenic Variant in Trans to alpha-Spectrin LELY Causing Neonatal Jaundice With Hemolytic Anemia From Hereditary Pyropoikilocytosis Coexisting With Gilbert Syndrome.
    Title: A Novel α-Spectrin Pathogenic Variant in Trans to α-Spectrin LELY Causing Neonatal Jaundice With Hemolytic Anemia From Hereditary Pyropoikilocytosis Coexisting With Gilbert Syndrome.
  8. Hereditary spherocytosis overlooked for 7 years in a pediatric patient with beta-thalassemia trait and novel compound heterozygous mutations of SPTA1 gene.
    Title: Hereditary spherocytosis overlooked for 7 years in a pediatric patient with β-thalassemia trait and novel compound heterozygous mutations of SPTA1 gene.
  9. A family affair-Severe fetal and neonatal hemolytic anemia due to novel alpha-spectrin mutations in two siblings.
    Title: A family affair-Severe fetal and neonatal hemolytic anemia due to novel alpha-spectrin mutations in two siblings.
  10. the molecular origin of chaperone activity resides in the surface exposed hydrophobic patches of the spectrin domains.
    Title: Localizing the chaperone activity of erythroid spectrin.
Submit: New GeneRIF Correction See all GeneRIFs (56)

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 2
MedGen: C1851741 OMIM: 130600 GeneReviews: Not available
Compare labs
Hereditary spherocytosis type 3
MedGen: C2678338 OMIM: 270970 GeneReviews: Not available
Compare labs
Pyropoikilocytosis, hereditary
MedGen: C0520739 OMIM: 266140 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Common variants at 10 genomic loci influence hemoglobin A₁(C) levels via glycemic and nonglycemic pathways.
EBI GWAS Catalog
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
EBI GWAS Catalog
Seventy-five genetic loci influencing the human red blood cell.
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
gag-pol HIV-1 protease cleaves alpha-spectrin in vitro at amino acid positions 1352, 1376, and 1697 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 filament binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 actin filament organization TAS
Traceable Author Statement
more info
 PubMed 
involved_in hemopoiesis IEA
Inferred from Electronic Annotation
more info
  
involved_in lymphocyte homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in plasma membrane organization IEA
Inferred from Electronic Annotation
more info
  
involved_in porphyrin-containing compound biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of T cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell shape IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in actin cytoskeleton TAS
Traceable Author Statement
more info
 PubMed 
located_in axon IEA
Inferred from Electronic Annotation
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 cuticular plate IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic side of plasma membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
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 alpha chain, erythrocytic 1
Names
alpha-I spectrin
elliptocytosis 2
erythroid alpha-spectrin
spectrin alpha 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_011474.1 RefSeqGene

    Range
    5002..81011
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1131

mRNA and Protein(s)

  1. NM_003126.4 → NP_003117.2  spectrin alpha chain, erythrocytic 1

    See identical proteins and their annotated locations for NP_003117.2

    Status: REVIEWED

    Source sequence(s)
    AL353894, BU665064, CD616351, M61877
    Consensus CDS
    CCDS41423.1
    UniProtKB/Swiss-Prot
    P02549, Q15514, Q5VYL1, Q5VYL2, Q6LDY5
    Related
    ENSP00000495214.1, ENST00000643759.2
    Conserved Domains (7) summary
    smart00150
    Location:902 → 958
    SPEC; Spectrin repeats
    cd00176
    Location:1608 → 1819
    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:1082 → 1179
    Spectrin; Spectrin repeat
    pfam08726
    Location:2350 → 2418
    EFhand_Ca_insen; Ca2+ insensitive EF hand
    pfam13499
    Location:2278 → 2343
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:2275 → 2343
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    cl17036
    Location:982 → 1033
    SH3; Src Homology 3 domain superfamily

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    158610704..158686715 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509916.3 → XP_011508218.1  spectrin alpha chain, erythrocytic 1 isoform X1

    See identical proteins and their annotated locations for XP_011508218.1

    UniProtKB/Swiss-Prot
    P02549, Q15514, Q5VYL1, Q5VYL2, Q6LDY5
    Conserved Domains (7) summary
    smart00150
    Location:902 → 958
    SPEC; Spectrin repeats
    cd00176
    Location:1608 → 1819
    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:1082 → 1179
    Spectrin; Spectrin repeat
    pfam08726
    Location:2350 → 2418
    EFhand_Ca_insen; Ca2+ insensitive EF hand
    pfam13499
    Location:2278 → 2343
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:2275 → 2343
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    cl17036
    Location:982 → 1033
    SH3; Src Homology 3 domain superfamily

  2. XM_047428883.1 → XP_047284839.1  spectrin alpha chain, erythrocytic 1 isoform X3

  3. XM_011509917.4 → XP_011508219.1  spectrin alpha chain, erythrocytic 1 isoform X2

    Conserved Domains (7) summary
    smart00150
    Location:902 → 958
    SPEC; Spectrin repeats
    cd00176
    Location:1608 → 1819
    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:1082 → 1179
    Spectrin; Spectrin repeat
    pfam08726
    Location:2344 → 2412
    EFhand_Ca_insen; Ca2+ insensitive EF hand
    pfam13499
    Location:2272 → 2337
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:2269 → 2337
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    cl17036
    Location:982 → 1033
    SH3; Src Homology 3 domain superfamily

  4. XM_011509918.4 → XP_011508220.1  spectrin alpha chain, erythrocytic 1 isoform X4

    Conserved Domains (4) summary
    smart00150
    Location:902 → 958
    SPEC; Spectrin repeats
    cd00176
    Location:1608 → 1819
    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:1928 → 2033
    Spectrin; Spectrin repeat
    cl17036
    Location:982 → 1033
    SH3; Src Homology 3 domain superfamily

  5. XM_011509919.4 → XP_011508221.1  spectrin alpha chain, erythrocytic 1 isoform X5

    Conserved Domains (4) summary
    smart00150
    Location:902 → 958
    SPEC; Spectrin repeats
    cd00176
    Location:266 → 476
    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:1082 → 1179
    Spectrin; Spectrin repeat
    cl17036
    Location:982 → 1033
    SH3; Src Homology 3 domain superfamily

  6. XM_047428888.1 → XP_047284844.1  spectrin alpha chain, erythrocytic 1 isoform X6

RNA

  1. XR_921911.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    157747803..157823815 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338464.1 → XP_054194439.1  spectrin alpha chain, erythrocytic 1 isoform X1

  2. XM_054338466.1 → XP_054194441.1  spectrin alpha chain, erythrocytic 1 isoform X3

  3. XM_054338465.1 → XP_054194440.1  spectrin alpha chain, erythrocytic 1 isoform X2

  4. XM_054338467.1 → XP_054194442.1  spectrin alpha chain, erythrocytic 1 isoform X5

  5. XM_054338468.1 → XP_054194443.1  spectrin alpha chain, erythrocytic 1 isoform X6

RNA

  1. XR_008486156.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P02549.5 GenPept UniProtKB/Swiss-Prot:P02549

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