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SPATA7 spermatogenesis associated 7 [ Homo sapiens (human) ]

Gene ID: 55812, updated on 22-Aug-2020

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
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

Genomic context

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See SPATA7 in Genome Data Viewer
Location:
14q31.3
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 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 EMAP like 5

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. Spectrum, frequency, and genotype-phenotype of mutations in SPATA7. Xiao X, et al. Mol Vis, 2019. PMID 31908400, Free PMC Article
  2. Phenotypic expansion and progression of SPATA7-associated retinitis pigmentosa. Sengillo JD, et al. Doc Ophthalmol, 2018 Apr. PMID 29411205, Free PMC Article
  3. Novel homozygous mutation in the SPATA7 gene causes autosomal recessive retinal degeneration in a consanguineous German family. Feldhaus B, et al. Ophthalmic Genet, 2018 Jan-Feb. PMID 28481129
  4. SPATA7: Evolving phenotype from cone-rod dystrophy to retinitis pigmentosa. Matsui R, et al. Ophthalmic Genet, 2016 Sep. PMID 26854980, Free PMC Article
  5. 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

See all (36) citations in PubMed

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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 <i>SPATA7</i>.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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
Genetics of coronary artery calcification among African Americans, a meta-analysis.
GeneReviews: Not available
Leber congenital amaurosis 3
MedGen: C1858677 OMIM: 604232 GeneReviews: Leber Congenital Amaurosis, Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview
Compare labs
Whole genome association scan for genetic polymorphisms influencing information processing speed.
GeneReviews: Not available

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

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
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
microtubule cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
photoreceptor cell maintenance IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
photoreceptor cell maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
protein localization to photoreceptor connecting cilium IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein localization to photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
  
protein localization to photoreceptor outer segment IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
axoneme IDA
Inferred from Direct Assay
more info
 PubMed 
ciliary basal body IBA
Inferred from Biological aspect of Ancestor
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
  

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_021183.1 RefSeqGene

    Range
    5001..57817
    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/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_018418.5 → 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
    Q9P0W8
    UniProtKB/TrEMBL
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 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, ENST00000045347.11
    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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