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SPATA7 spermatogenesis associated 7 [ Homo sapiens (human) ]

Gene ID: 55812, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (88385657..88470350)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (82606616..82691159)
105.20220307 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 uncharacterized LOC105370612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8835 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: 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. SPATA7-Associated Juvenile Retinitis Pigmentosa in Two Brothers from a Consanguineous Iraqi Family in Switzerland. Yahya F, et al. Klin Monbl Augenheilkd, 2023 Apr. PMID 37164434
  2. Spectrum, frequency, and genotype-phenotype of mutations in SPATA7. Xiao X, et al. Mol Vis, 2019. PMID 31908400, Free PMC Article
  3. Phenotypic expansion and progression of SPATA7-associated retinitis pigmentosa. Sengillo JD, et al. Doc Ophthalmol, 2018 Apr. PMID 29411205, Free PMC Article
  4. 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
  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

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)

Genotypes

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 response to stimulus IEA
Inferred from Electronic Annotation
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_2023_10

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

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

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

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

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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