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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
    mouse all
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    Genomic context

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    See SPTA1 in Genome Data Viewer
    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

    Gene LinkOut

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