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    SPATA7 spermatogenesis associated 7 [ Homo sapiens (human) ]

    Gene ID: 55812, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SPATA7provided by HGNC
    Official Full Name
    spermatogenesis associated 7provided by HGNC
    Primary source
    HGNC:HGNC:20423
    See related
    Ensembl:ENSG00000042317 MIM:609868; AllianceGenome:HGNC:20423
    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
    HSD3; LCA3; RP94; HSD-3.1; HEL-S-296
    Summary
    This gene, originally isolated from testis, is also expressed in retina. Mutations in this gene are associated with Leber congenital amaurosis and juvenile retinitis pigmentosa. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
    Expression
    Broad expression in testis (RPKM 22.8), thyroid (RPKM 6.0) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPATA7 in Genome Data Viewer
    Location:
    14q31.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (88385657..88470350)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (82606616..82691159)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (88852001..88904804)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8835 Neighboring gene KCNK10 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5989 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38654 Neighboring gene Sharpr-MPRA regulatory region 1231 Neighboring gene potassium two pore domain channel subfamily K member 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:88685623-88685838 Neighboring gene Sharpr-MPRA regulatory region 1180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:88788959-88789618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:88792556-88793070 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:88830965-88831772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8840 Neighboring gene NANOG hESC enhancer GRCh37_chr14:88948745-88949275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8841 Neighboring gene protein tyrosine phosphatase non-receptor type 21 Neighboring gene uncharacterized LOC105370614 Neighboring gene RNA, U4 small nuclear 22, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89015655-89016472 Neighboring gene proline-rich protein 2-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5991

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Novel homozygous large deletion including the 5' part of the SPATA7 gene in a consanguineous Israeli Muslim Arab family. Mayer AK, et al. Mol Vis, 2015. PMID 25814828, Free PMC Article
    2. Spectrum of SPATA7 mutations in Leber congenital amaurosis and delineation of the associated phenotype. Perrault I, et al. Hum Mutat, 2010 Mar. PMID 20104588
    3. Screening of SPATA7 in patients with Leber congenital amaurosis and severe childhood-onset retinal dystrophy reveals disease-causing mutations. Mackay DS, et al. Invest Ophthalmol Vis Sci, 2011 May 9. PMID 21310915
    4. Late onset retinitis pigmentosa. Avila-Fernández A, et al. Ophthalmology, 2011 Dec. PMID 22136677
    5. SPATA7: Evolving phenotype from cone-rod dystrophy to retinitis pigmentosa. Matsui R, et al. Ophthalmic Genet, 2016 Sep. PMID 26854980, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SPATA7-Associated Juvenile Retinitis Pigmentosa in Two Brothers from a Consanguineous Iraqi Family in Switzerland.
      Title: SPATA7-Associated Juvenile Retinitis Pigmentosa in Two Brothers from a Consanguineous Iraqi Family in Switzerland.
    2. Narrow arterioles, a relatively well-preserved macular region, and widespread retinal pigment epithelium atrophy resulting in diffuse mottling hypopigmentation in the midperipheral retina may be considered early and common fundus changes specific to SPATA7-associated retinopathy.
      Title: Spectrum, frequency, and genotype-phenotype of mutations in SPATA7.
    3. Compound heterozygous c.1100A > G, p.(Y367C) and c.1102_1103delCT, p.(L368Efs*4) variants in SPATA7 manifest as an unusual RP phenotype in this case, showing extensive choroidal sclerosis and retinal pigment epithelium (RPE) atrophy with evidence of progression over two years on multimodal imaging.
      Title: Phenotypic expansion and progression of SPATA7-associated retinitis pigmentosa.
    4. We present the clinical and genetic findings of two siblings harboring the c.1112T>C/p.I371T homozygous mutation in the SPATA7 gene.
      Title: Novel homozygous mutation in the SPATA7 gene causes autosomal recessive retinal degeneration in a consanguineous German family.
    5. The disease resulting from SPATA7 mutations in this patient initially presented as a cone-rod dystrophy (CRD), but changed over time into a phenotype more reminiscent of late-stage retinitis pigmentosa (RP).
      Title: SPATA7: Evolving phenotype from cone-rod dystrophy to retinitis pigmentosa.
    6. SPATA7 plays a role in RPGRIP1-mediated protein trafficking across the connecting cilium of photoreceptor cells. Apoptotic degeneration of these cells triggered by protein mislocalization is a mechanism of disease progression in LCA3/juvenile RP patients
      Title: Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina.
    7. A novel homozygous large deletion in SPATA7 associated with juvenile retinitis pigmentosa has been found in a consanguineous Israeli Muslim Arab family.
      Title: Novel homozygous large deletion including the 5' part of the SPATA7 gene in a consanguineous Israeli Muslim Arab family.
    8. Digenic and triallelic mutations of CRB1 and SPATA7 were detected in a Chinese family with Leber congenital amaurosis. The results imply that CRB1 and SPATA7 may not interact with each other directly.
      Title: Lack of phenotypic effect of triallelic variation in SPATA7 in a family with Leber congenital amaurosis resulting from CRB1 mutations.
    9. In conclusion, our data established the first linkage association of a loss-of-function mutation in the SPATA7 gene with a typical retinitis pigmentosa (RP) phenotype and not with leber congenital amaurosis or early onset RP.
      Title: Late onset retinitis pigmentosa.
    10. Mutations in SPATA7 are a rare cause of childhood retinal dystrophy accounting for 1.7% of disease in this cohort.
      Title: Screening of SPATA7 in patients with Leber congenital amaurosis and severe childhood-onset retinal dystrophy reveals disease-causing mutations.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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
    Leber congenital amaurosis 3
    MedGen: C1858677 OMIM: 604232 GeneReviews: Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview
    		not available

    EBI GWAS Catalog

    Description
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Whole genome association scan for genetic polymorphisms influencing information processing speed.
    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)

    Pathways from PubChem

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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

    Homology

    Clone Names

    • MGC102934, DKFZp686D07199

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in microtubule cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in photoreceptor cell maintenance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in photoreceptor cell maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein localization to photoreceptor connecting cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein localization to photoreceptor outer segment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axoneme IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in photoreceptor connecting cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in photoreceptor distal connecting cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in rod photoreceptor outer segment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    spermatogenesis-associated protein 7
    Names
    epididymis secretory protein Li 296
    epididymis secretory sperm binding protein
    spermatogenesis-associated protein HSD3

    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_021183.2 RefSeqGene

      Range
      5002..57805
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001040428.4 → NP_001035518.1  spermatogenesis-associated protein 7 isoform 2

      See identical proteins and their annotated locations for NP_001035518.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is lacking an in-frame coding exon compared to variant 1, resulting in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AL049834
      Consensus CDS
      CCDS32132.1
      UniProtKB/TrEMBL
      A8K3L6
      Related
      ENSP00000348991.5, ENST00000356583.9
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 388
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    2. NM_018418.5 → NP_060888.2  spermatogenesis-associated protein 7 isoform 1

      See identical proteins and their annotated locations for NP_060888.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL049834
      Consensus CDS
      CCDS9883.1
      UniProtKB/Swiss-Prot
      Q5BKY5, Q8WX30, Q96HF3, Q9H0X0, Q9P0W7, Q9P0W8
      UniProtKB/TrEMBL
      A0A384MEC0, V9HVY9
      Related
      ENSP00000377176.4, ENST00000393545.9
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 420
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    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

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      88385657..88470350
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006720205.2 → XP_006720268.1  spermatogenesis-associated protein 7 isoform X6

      Conserved Domains (1) summary
      pfam15244
      Location:10 → 421
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    2. XM_047431581.1 → XP_047287537.1  spermatogenesis-associated protein 7 isoform X7

      Related
      ENSP00000045347.7, ENST00000045347.11

    3. XM_047431584.1 → XP_047287540.1  spermatogenesis-associated protein 7 isoform X9

    4. XM_006720204.2 → XP_006720267.1  spermatogenesis-associated protein 7 isoform X5

      Conserved Domains (1) summary
      pfam15244
      Location:10 → 421
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    5. XM_047431582.1 → XP_047287538.1  spermatogenesis-associated protein 7 isoform X8

    6. XM_005267851.2 → XP_005267908.1  spermatogenesis-associated protein 7 isoform X1

      UniProtKB/TrEMBL
      A0A384MEC0
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 421
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    7. XM_005267852.3 → XP_005267909.1  spermatogenesis-associated protein 7 isoform X2

      UniProtKB/TrEMBL
      A8K3L6
      Conserved Domains (1) summary
      pfam15244
      Location:10 → 389
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    8. XM_011536952.2 → XP_011535254.1  spermatogenesis-associated protein 7 isoform X3

      UniProtKB/TrEMBL
      A8K3L6
      Conserved Domains (1) summary
      pfam15244
      Location:4 → 364
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    9. XM_024449660.2 → XP_024305428.1  spermatogenesis-associated protein 7 isoform X4

      UniProtKB/TrEMBL
      A8K3L6
      Conserved Domains (1) summary
      pfam15244
      Location:4 → 363
      HSD3; Spermatogenesis-associated protein 7, or HSD3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      82606616..82691159
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376382.1 → XP_054232357.1  spermatogenesis-associated protein 7 isoform X6

    2. XM_054376383.1 → XP_054232358.1  spermatogenesis-associated protein 7 isoform X7

    3. XM_054376385.1 → XP_054232360.1  spermatogenesis-associated protein 7 isoform X9

    4. XM_054376381.1 → XP_054232356.1  spermatogenesis-associated protein 7 isoform X5

    5. XM_054376384.1 → XP_054232359.1  spermatogenesis-associated protein 7 isoform X8

    6. XM_054376377.1 → XP_054232352.1  spermatogenesis-associated protein 7 isoform X1

      UniProtKB/TrEMBL
      A0A384MEC0

    7. XM_054376378.1 → XP_054232353.1  spermatogenesis-associated protein 7 isoform X2

      UniProtKB/TrEMBL
      A8K3L6

    8. XM_054376379.1 → XP_054232354.1  spermatogenesis-associated protein 7 isoform X3

      UniProtKB/TrEMBL
      A8K3L6

    9. XM_054376380.1 → XP_054232355.1  spermatogenesis-associated protein 7 isoform X4

      UniProtKB/TrEMBL
      A8K3L6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P0W8.3 GenPept UniProtKB/Swiss-Prot:Q9P0W8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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