SPAG17 sperm associated antigen 17 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPAG17provided by HGNC
Official Full Name: sperm associated antigen 17provided by HGNC
Primary source: HGNC:HGNC:26620
See related: Ensembl:ENSG00000155761 MIM:616554; AllianceGenome:HGNC:26620
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: PF6; CT143; SPGF55
Summary: This gene encodes a central pair protein present in the axonemes of cells with a "9 + 2" organization of microtubules. The encoded protein is required for the proper function of the axoneme. Mutations in the orthologous gene in mice lead to primary ciliary dyskinesia characterized by immotile nasal and tracheal cilia, reduced clearance of nasal mucus, profound respiratory distress, hydrocephalus, and neonatal lethality within twelve hours of birth due to impaired airway mucociliary clearance. Single-nucleotide polymorphisms in this gene are associated with human height and targeted mutations lead to skeletal malformations affecting the limbs in mice, suggesting a role for this gene in skeletal development. [provided by RefSeq, Feb 2017]
Expression: Biased expression in testis (RPKM 9.4), esophagus (RPKM 2.4) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p12

Exon count:: 56

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (117953590..118185228, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (117962843..118194535, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (118496213..118727851, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Reduced SPAG17 Expression in Systemic Sclerosis Triggers Myofibroblast Transition and Drives Fibrosis.
Title: Reduced SPAG17 Expression in Systemic Sclerosis Triggers Myofibroblast Transition and Drives Fibrosis.
Alterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA-Sequencing Analysis in Patients With Systemic Sclerosis.
Title: Alterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA-Sequencing Analysis in Patients With Systemic Sclerosis.
In silico analysis revealed that R1448Q is a potential pathogenic mutation. Immunostaining and western blot assays showed that the R1448Q mutation may exert a negative effect on the steady-state of the SPAG17 protein. Therefore, SPAG17 may be a new pathogenic gene causing Asthenozoospermia (AZS) .
Title: A familial study of twins with severe asthenozoospermia identified a homozygous SPAG17 mutation by whole-exome sequencing.
Homozygous missense mutation in SPAG17 gene is associated with multiple congenital anomalies, including brain malformations and skeletal dysplasia suggestive of cranioectodermal dysplasia ciliopathy.
Title: Uncommon runs of homozygosity disclose homozygous missense mutations in two ciliopathy-related genes (SPAG17 and WDR35) in a patient with multiple brain and skeletal anomalies.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Identification of 15 loci influencing height in a Korean population.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study.

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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
Spermatogenic failure 55 MedGen: C5543580 OMIM: 619380 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study identifies two risk loci for congenital heart malformations in Han Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
A novel common variant in DCST2 is associated with length in early life and height in adulthood. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 20 loci that influence adult height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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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Markers

WDR3__5087 (e-PCR)
- UniSTS:466558

AL009508 (e-PCR)
- UniSTS:60063

AL009658 (e-PCR)
- UniSTS:67744

PF6__5669 (e-PCR)
- UniSTS:463793

NoName (e-PCR)
- UniSTS:64952

AL033783 (e-PCR)
- UniSTS:93635

D1S2669 (e-PCR), detects polymorphism
- UniSTS:59900

Clone Names

FLJ34497, FLJ44343, FLJ44353, DKFZp434B0610

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in axonemal central apparatus assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in epithelial cilium movement involved in extracellular fluid movement	IBA Inferred from Biological aspect of Ancestor more info
involved_in intramanchette transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in manchette assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in motile cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in acrosomal vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in axonemal central apparatus	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in manchette	ISS Inferred from Sequence or Structural Similarity more info
located_in microtubule	IEA Inferred from Electronic Annotation more info
located_in motile cilium	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sperm-associated antigen 17

Names: projection protein PF6 homolog

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_053041.1 RefSeqGene

Range

4998..236636

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_206996.4 → NP_996879.1 sperm-associated antigen 17

See identical proteins and their annotated locations for NP_996879.1

Status: REVIEWED

Source sequence(s)

AL121993, AL513191, AY555274, DB060943, DB340825

Consensus CDS

CCDS899.1

UniProtKB/Swiss-Prot

Q6Q759, Q8NAZ1, Q9NT21

Related

ENSP00000337804.5, ENST00000336338.10

Conserved Domains (2) summary

pfam04004
Location:248 → 346

Leo1; Leo1-like protein

pfam14874
Location:2076 → 2180

PapD-like; Flagellar-associated PapD-like

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

117953590..118185228 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006710427.4 → XP_006710490.1 sperm-associated antigen 17 isoform X4

Conserved Domains (1) summary

pfam14874
Location:2011 → 2115

PapD-like; Flagellar-associated PapD-like
XM_006710426.4 → XP_006710489.1 sperm-associated antigen 17 isoform X2

Conserved Domains (2) summary

pfam04004
Location:248 → 346

Leo1; Leo1-like protein

pfam14874
Location:2038 → 2142

PapD-like; Flagellar-associated PapD-like
XM_011540934.2 → XP_011539236.1 sperm-associated antigen 17 isoform X3

Conserved Domains (2) summary

pfam04004
Location:248 → 346

Leo1; Leo1-like protein

pfam14874
Location:2032 → 2136

PapD-like; Flagellar-associated PapD-like
XM_011540935.3 → XP_011539237.1 sperm-associated antigen 17 isoform X5

Conserved Domains (2) summary

pfam04004
Location:135 → 233

Leo1; Leo1-like protein

pfam14874
Location:1963 → 2067

PapD-like; Flagellar-associated PapD-like
XM_011540937.3 → XP_011539239.1 sperm-associated antigen 17 isoform X6

See identical proteins and their annotated locations for XP_011539239.1

Conserved Domains (1) summary

pfam14874
Location:1526 → 1630

PapD-like; Flagellar-associated PapD-like
XM_047448734.1 → XP_047304690.1 sperm-associated antigen 17 isoform X6
XM_011540936.3 → XP_011539238.1 sperm-associated antigen 17 isoform X6

See identical proteins and their annotated locations for XP_011539238.1

Conserved Domains (1) summary

pfam14874
Location:1526 → 1630

PapD-like; Flagellar-associated PapD-like
XM_047448753.1 → XP_047304709.1 sperm-associated antigen 17 isoform X8
XM_006710428.4 → XP_006710491.1 sperm-associated antigen 17 isoform X7

See identical proteins and their annotated locations for XP_006710491.1

Conserved Domains (1) summary

pfam14874
Location:1349 → 1453

PapD-like; Flagellar-associated PapD-like
XM_011540942.3 → XP_011539244.1 sperm-associated antigen 17 isoform X8

See identical proteins and their annotated locations for XP_011539244.1

Conserved Domains (1) summary

pfam14874
Location:1315 → 1419

PapD-like; Flagellar-associated PapD-like
XM_011540939.3 → XP_011539241.1 sperm-associated antigen 17 isoform X7

See identical proteins and their annotated locations for XP_011539241.1

Conserved Domains (1) summary

pfam14874
Location:1349 → 1453

PapD-like; Flagellar-associated PapD-like
XM_047448758.1 → XP_047304714.1 sperm-associated antigen 17 isoform X9
XM_047448722.1 → XP_047304678.1 sperm-associated antigen 17 isoform X1

UniProtKB/Swiss-Prot

Q6Q759, Q8NAZ1, Q9NT21