SPATA16 spermatogenesis associated 16 [Homo sapiens (human)] - Gene

Summary

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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SPATA16 promoter hypermethylation and downregulation in male infertility.
Title: SPATA16 promoter hypermethylation and downregulation in male infertility.
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.
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.
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.
Mutation of SPATA16 is associated with globozoospermia.
Title: A new mutation identified in SPATA16 in two globozoospermic patients.
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.
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.
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.
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.
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.

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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	Compare labs

EBI GWAS Catalog

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

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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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

NG_021422.1 RefSeqGene

Range

5034..256912

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

172889357..173141235 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

175675113..175927030 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B3KS78
XM_054348066.1 → XP_054204041.1 spermatogenesis-associated protein 16 isoform X2