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SPATA16 spermatogenesis associated 16 [ Homo sapiens (human) ]

Gene ID: 83893, updated on 27-Nov-2024

Summary

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Official Symbol
SPATA16provided by HGNC
Official Full Name
spermatogenesis associated 16provided by HGNC
Primary source
HGNC:HGNC:29935
See related
Ensembl:ENSG00000144962 MIM:609856; AllianceGenome:HGNC:29935
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
SPGF6; NYD-SP12
Summary
This gene encodes a testis-specific protein that belongs to the tetratricopeptide repeat-like superfamily. The encoded protein localizes to the Golgi apparatus and may play a role in spermatogenesis. [provided by RefSeq, May 2010]
Expression
Restricted expression toward testis (RPKM 29.2) See more
Orthologs
mouse all
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Genomic context

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See SPATA16 in Genome Data Viewer
Location:
3q26.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (172889357..173141235, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (175675113..175927030, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (172607147..172859025, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986052 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:172571656-172572164 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:172572165-172572672 Neighboring gene NANOG hESC enhancer GRCh37_chr3:172579049-172579639 Neighboring gene MMACHC pseudogene 1 Neighboring gene MPRA-validated peak4926 silencer Neighboring gene uncharacterized LOC105374221 Neighboring gene small nucleolar RNA U13 Neighboring gene uncharacterized LOC105374220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:172858511-172859012 Neighboring gene uncharacterized LOC105374224 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:172963126-172963695 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:172971223-172971761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:173004473-173004973 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:173070760-173071467 Neighboring gene uncharacterized LOC124909458

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. Comparison of sperm morphology and nuclear sperm quality in SPATA16- and DPY19L2-mutated globozoospermic patients. Ghédir H, et al. Andrologia, 2019 Jul. PMID 30912172
  2. Gene functional research using polyethylenimine-mediated in vivo gene transfection into mouse spermatogenic cells. Lu L, et al. Asian J Androl, 2006 Jan. PMID 16372119
  3. Rapid evolution, genetic variations, and functional association of the human spermatogenesis-related gene NYD-SP12. Zhang Q, et al. J Mol Evol, 2007 Aug. PMID 17665087
  4. A new mutation identified in SPATA16 in two globozoospermic patients. ElInati E, et al. J Assist Reprod Genet, 2016 Jun. PMID 27086357, Free PMC Article
  5. Homozygous mutation in SPATA16 is associated with male infertility in human globozoospermia. Dam AH, et al. Am J Hum Genet, 2007 Oct. PMID 17847006, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SPATA16 promoter hypermethylation and downregulation in male infertility.
    Title: SPATA16 promoter hypermethylation and downregulation in male infertility.
  2. Association of CATSPER1, SPATA16 and TEX11 genes polymorphism with idiopathic azoospermia and oligospermia risk in Iranian population.
    Title: Association of CATSPER1, SPATA16 and TEX11 genes polymorphism with idiopathic azoospermia and oligospermia risk in Iranian population.
  3. Study showed that SPATA16 defects could be associated with an abnormal meiosis leading to a particular morphological sperm defect of double/multiple round-headed and multi-flagella and a higher sperm aneuploidy rate than in case of DPY19L2-defects in classic globozoospermia.
    Title: Comparison of sperm morphology and nuclear sperm quality in SPATA16- and DPY19L2-mutated globozoospermic patients.
  4. This study demonstrates that Spata16 is indispensable for male fertility in mice, as well as in humans.
    Title: Human Globozoospermia-Related Gene Spata16 Is Required for Sperm Formation Revealed by CRISPR/Cas9-Mediated Mouse Models.
  5. Mutation of SPATA16 is associated with globozoospermia.
    Title: A new mutation identified in SPATA16 in two globozoospermic patients.
  6. Case Report: report of a pregnancy obtained in a man with homozygous SPATA16 mutated globozoospermia.
    Title: First successful pregnancy in a globozoospermic patient having homozygous mutation in SPATA16.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  8. Results indicate that NYD-SP12 evolves rapidly in both the human and the chimpanzee lineages, which is likely caused by Darwinian positive selection and/or sexual selection.
    Title: Rapid evolution, genetic variations, and functional association of the human spermatogenesis-related gene NYD-SP12.
  9. consanguineous family with three affected brothers, in whom we have identified a homozygous mutation in the spermatogenesis-specific gene SPATA16. This is the first example of a nonsyndromic male infertility condition caused by an autosomal gene defect.
    Title: Homozygous mutation in SPATA16 is associated with male infertility in human globozoospermia.
  10. results suggest that NYD-SP12 is involved in spermatogenesis, and that NYD-SP12-encoded protein might function in the Golgi apparatus
    Title: Identification and characterization of a novel human testis-specific Golgi protein, NYD-SP12.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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
Globozoospermia
MedGen: C0403825 OMIM: 102530 GeneReviews: Not available
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EBI GWAS Catalog

Description
A genome-wide association meta-analysis of preschool internalizing problems.
EBI GWAS Catalog
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
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)

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

Process Evidence Code Pubs
involved_in spermatid development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in acrosomal vesicle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
spermatogenesis-associated protein 16
Names
testicular tissue protein Li 185
testis development protein NYD-SP12
testis-specific Golgi protein

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_021422.1 RefSeqGene

    Range
    5034..256912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_031955.6 → NP_114161.3  spermatogenesis-associated protein 16

    See identical proteins and their annotated locations for NP_114161.3

    Status: REVIEWED

    Source sequence(s)
    AC063933, BC034496, BI829426
    Consensus CDS
    CCDS3221.1
    UniProtKB/Swiss-Prot
    Q0R0N4, Q0R0S0, Q0R0W2, Q0R129, Q0R131, Q0R140, Q0R1B8, Q0R1G5, Q0R1I2, Q0R1J6, Q0R1S4, Q0R202, Q0R280, Q0R2F8, Q0R2N6, Q0R2N7, Q0R2R0, Q0R2R1, Q0R2S3, Q0R2S4, Q0R2S5, Q0R2T4, Q0R2T7, Q0R2U2, Q0R2U8, Q0R2U9, Q0R2V5, Q0R2V7, Q8NE67, Q9BXB7
    UniProtKB/TrEMBL
    A0A140VJV8, B3KS78
    Related
    ENSP00000341765.3, ENST00000351008.4
    Conserved Domains (2) summary
    sd00006
    Location:217 → 257
    TPR; TPR repeat [structural motif]
    pfam15015
    Location:6 → 567
    NYD-SP12_N; Spermatogenesis-associated, N-terminal

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    172889357..173141235 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713778.4 → XP_006713841.1  spermatogenesis-associated protein 16 isoform X1

    UniProtKB/TrEMBL
    B3KS78
    Conserved Domains (2) summary
    sd00006
    Location:217 → 257
    TPR; TPR repeat [structural motif]
    pfam15015
    Location:6 → 529
    NYD-SP12_N; Spermatogenesis-associated, N-terminal

  2. XM_017007308.3 → XP_016862797.1  spermatogenesis-associated protein 16 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    175675113..175927030 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348065.1 → XP_054204040.1  spermatogenesis-associated protein 16 isoform X1

  2. XM_054348066.1 → XP_054204041.1  spermatogenesis-associated protein 16 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BXB7.3 GenPept UniProtKB/Swiss-Prot:Q9BXB7

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