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SPATA7 spermatogenesis associated 7 [ Homo sapiens (human) ]

Gene ID: 55812, updated on 3-Jun-2018
Official Symbol
SPATA7provided by HGNC
Official Full Name
spermatogenesis associated 7provided by HGNC
Primary source
HGNC:HGNC:20423
See related
Ensembl:ENSG00000042317 MIM:609868; Vega:OTTHUMG00000170744
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; 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
See SPATA7 in Genome Data Viewer
Location:
14q31.3
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (88385638..88470350)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (88851982..88904804)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370613 Neighboring gene uncharacterized LOC105370612 Neighboring gene potassium two pore domain channel subfamily K member 10 Neighboring gene uncharacterized LOC105370614 Neighboring gene protein tyrosine phosphatase, non-receptor type 21 Neighboring gene RNA, U4 small nuclear 22, pseudogene Neighboring gene zinc finger CCCH-type containing 14 Neighboring gene echinoderm microtubule associated protein like 5

Go to nucleotide: Graphics FASTA GenBank

  • 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 Jun 15 11:32:44 2016

Related articles in PubMed

  1. SPATA7: Evolving phenotype from cone-rod dystrophy to retinitis pigmentosa. Matsui R, et al. Ophthalmic Genet, 2016 Sep. PMID 26854980, Free PMC Article
  2. 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
  3. Late onset retinitis pigmentosa. Avila-Fernández A, et al. Ophthalmology, 2011 Dec. PMID 22136677
  4. 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
  5. Spectrum of SPATA7 mutations in Leber congenital amaurosis and delineation of the associated phenotype. Perrault I, et al. Hum Mutat, 2010 Mar. PMID 20104588

See all (28) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. analysis of the SPATA7 mutations in Leber congenital amaurosis and the associated phenotype
    Title: Spectrum of SPATA7 mutations in Leber congenital amaurosis and delineation of the associated phenotype.
  8. Spata7 is expressed in the mature mouse retina.
    Title: Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa.
  9. isolation and characterization of HSD-3.1 expressed in the testis
    Title: A novel gene, RSD-3/HSD-3.1, encodes a meiotic-related protein expressed in rat and human testis.
Submit: New GeneRIF Correction

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
Compare labs

NHGRI GWAS Catalog

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

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC102934, DKFZp686D07199

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
photoreceptor cell maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
protein localization to photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
  
protein localization to photoreceptor outer segment ISS
Inferred from Sequence or Structural Similarity
more info
  
response to stimulus IEA
Inferred from Electronic Annotation
more info
  
visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
axoneme IDA
Inferred from Direct Assay
more info
 PubMed 
ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
cytosol IDA
Inferred from Direct Assay
more info
  
microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
  
nucleoplasm IDA
Inferred from Direct Assay
more info
  
photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
  
Preferred Names
spermatogenesis-associated protein 7
Names
epididymis secretory protein Li 296
spermatogenesis-associated protein HSD3

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_021183.1 RefSeqGene

    Range
    5001..57817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001040428.3 → 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)
    AF144487, BC008656, BC090875, DA568174
    Consensus CDS
    CCDS32132.1
    UniProtKB/Swiss-Prot
    Q9P0W8
    Related
    ENSP00000348991.5, ENST00000356583.9
    Conserved Domains (1) summary
    pfam15244
    Location:10 → 388
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  2. NM_018418.4 → 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)
    AF144487, BC008656, BC090875, DA568174
    Consensus CDS
    CCDS9883.1
    UniProtKB/Swiss-Prot
    Q9P0W8
    UniProtKB/TrEMBL
    V9HVY9
    Related
    ENSP00000377176.4, OTTHUMP00000244292, ENST00000393545.8, OTTHUMT00000410172
    Conserved Domains (1) summary
    pfam15244
    Location:10 → 420
    HSD3; Spermatogenesis-associated protein 7, or HSD3

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    88385638..88470350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536953.1 → XP_011535255.1  spermatogenesis-associated protein 7 isoform X9

    Conserved Domains (1) summary
    pfam15244
    Location:1 → 315
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  2. XM_017021457.1 → XP_016876946.1  spermatogenesis-associated protein 7 isoform X10

  3. XM_005267855.1 → XP_005267912.1  spermatogenesis-associated protein 7 isoform X7

    See identical proteins and their annotated locations for XP_005267912.1

    Conserved Domains (1) summary
    pfam15244
    Location:17 → 357
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  4. XM_017021455.1 → XP_016876944.1  spermatogenesis-associated protein 7 isoform X8

  5. XM_005267852.2 → XP_005267909.1  spermatogenesis-associated protein 7 isoform X2

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

  6. XM_006720205.1 → XP_006720268.1  spermatogenesis-associated protein 7 isoform X12

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

  7. XM_006720204.1 → XP_006720267.1  spermatogenesis-associated protein 7 isoform X11

    Related
    ENSP00000045347.7, OTTHUMP00000244304, ENST00000045347.11, OTTHUMT00000410187
    Conserved Domains (1) summary
    pfam15244
    Location:10 → 421
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  8. XM_011536951.1 → XP_011535253.1  spermatogenesis-associated protein 7 isoform X3

    Conserved Domains (1) summary
    pfam15244
    Location:1 → 370
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  9. XM_017021452.1 → XP_016876941.1  spermatogenesis-associated protein 7 isoform X4

    Conserved Domains (1) summary
    pfam15244
    Location:1 → 369
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  10. XM_017021453.1 → XP_016876942.1  spermatogenesis-associated protein 7 isoform X7

    Conserved Domains (1) summary
    pfam15244
    Location:17 → 357
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  11. XM_005267854.1 → XP_005267911.1  spermatogenesis-associated protein 7 isoform X7

    See identical proteins and their annotated locations for XP_005267911.1

    Conserved Domains (1) summary
    pfam15244
    Location:17 → 357
    HSD3; Spermatogenesis-associated protein 7, or HSD3

  12. XM_017021454.1 → XP_016876943.1  spermatogenesis-associated protein 7 isoform X8

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

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

  14. XM_011536952.1 → XP_011535254.1  spermatogenesis-associated protein 7 isoform X5

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

  15. XM_024449660.1 → XP_024305428.1  spermatogenesis-associated protein 7 isoform X6

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

  16. XM_017021456.1 → XP_016876945.1  spermatogenesis-associated protein 7 isoform X8

RNA

  1. XR_002957563.1 RNA Sequence

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

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

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