SPATA7 spermatogenesis associated 7 [Homo sapiens (human)] - Gene

Summary

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

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_000014.9 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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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

Associated conditions

Description	Tests
Leber congenital amaurosis 3 MedGen: C1858677 OMIM: 604232 GeneReviews: Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview	Compare labs

EBI GWAS Catalog

Description
Genetics of coronary artery calcification among African Americans, a meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Whole genome association scan for genetic polymorphisms influencing information processing speed. 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

WI-14643 (e-PCR)
- UniSTS:60982

SHGC-148790 (e-PCR)
- UniSTS:176610

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

NG_021183.2 RefSeqGene

Range

5002..57805

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

88385657..88470350

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047431581.1 → XP_047287537.1 spermatogenesis-associated protein 7 isoform X7

Related

ENSP00000045347.7, ENST00000045347.11
XM_047431584.1 → XP_047287540.1 spermatogenesis-associated protein 7 isoform X9
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
XM_047431582.1 → XP_047287538.1 spermatogenesis-associated protein 7 isoform X8
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
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
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
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