Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55812
Gene name Gene Name - the full gene name approved by the HGNC.	Spermatogenesis associated 7
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SPATA7
Synonyms (NCBI Gene) Gene synonyms aliases	HEL-S-296, HSD-3.1, HSD3, LCA3, RP94
Chromosome Chromosome number	14
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	14q31.3
Summary Summary of gene provided in NCBI Entrez Gene.	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 be

Show/Hide all(20)

SNP ID	Visualize variation	Clinical significance	Consequence
rs75895925	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs80044281	C>A,T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant, synonymous variant, non coding transcript variant
rs138190453	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs138993523	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs140287375	C>G,T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant, missense variant, non coding transcript variant, 5 prime UTR variant
rs149478294	A>G	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, coding sequence variant, missense variant, downstream transcript variant
rs371609982	G>A,C,T	Pathogenic, uncertain-significance	Upstream transcript variant, coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs374268850	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs386834241	->A	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs386834243	A>-	Pathogenic	Downstream transcript variant, coding sequence variant, genic downstream transcript variant, intron variant, frameshift variant
rs567890014	TT>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs753697847	T>-	Pathogenic	Downstream transcript variant, genic downstream transcript variant, intron variant, frameshift variant, coding sequence variant
rs766017194	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Downstream transcript variant, genic downstream transcript variant, synonymous variant, intron variant, coding sequence variant, missense variant
rs767745816	T>A	Pathogenic, likely-pathogenic	Stop gained, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs768028061	G>A,T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, synonymous variant
rs777069665	CT>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs786204787	T>C	Likely-pathogenic	Intron variant, splice donor variant
rs878853385	->C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1555370458	TCTCT>-	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, frameshift variant
rs1595158200	GCAGCCGGAGAGGTAAAGGGCAGCTG>-	Pathogenic	Upstream transcript variant, coding sequence variant, 5 prime UTR variant, intron variant, genic upstream transcript variant, splice donor variant, non coding transcript variant

Show/Hide all(26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000226	Process	Microtubule cytoskeleton organization	IBA
GO:0000226	Process	Microtubule cytoskeleton organization	IEA
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0005515	Function	Protein binding	IPI	25398945
GO:0005737	Component	Cytoplasm	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005930	Component	Axoneme	IBA
GO:0005930	Component	Axoneme	IDA	25398945
GO:0007601	Process	Visual perception	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA	25398945
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0036064	Component	Ciliary basal body	IBA
GO:0036064	Component	Ciliary basal body	IDA	25398945
GO:0042995	Component	Cell projection	IEA
GO:0045494	Process	Photoreceptor cell maintenance	IBA
GO:0045494	Process	Photoreceptor cell maintenance	IEA
GO:0045494	Process	Photoreceptor cell maintenance	ISS
GO:0120200	Component	Rod photoreceptor outer segment	IBA
GO:0120200	Component	Rod photoreceptor outer segment	IEA
GO:0120206	Component	Photoreceptor distal connecting cilium	IBA
GO:0120206	Component	Photoreceptor distal connecting cilium	IEA
GO:1903546	Process	Protein localization to photoreceptor outer segment	IEA
GO:1903546	Process	Protein localization to photoreceptor outer segment	ISS
GO:1903621	Process	Protein localization to photoreceptor connecting cilium	IEA
GO:1903621	Process	Protein localization to photoreceptor connecting cilium	ISS

MIM	HGNC	e!Ensembl
609868	20423	ENSG00000042317

Protein

UniProt ID

Q9P0W8

Protein name

Spermatogenesis-associated protein 7 (HSD-3.1) (Spermatogenesis-associated protein HSD3)

Protein function

Involved in the maintenance of both rod and cone photoreceptor cells (By similarity). It is required for recruitment and proper localization of RPGRIP1 to the photoreceptor connecting cilium (CC), as well as photoreceptor-specific localization o

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF15244	HSD3	9 → 422	Spermatogenesis-associated protein 7, or HSD3	Family

Sequence

MDGSRRVRATSVLPRYGPPCLFKGHLSTKSNAFCTDSSSLRLSTLQLVKNHMAVHYNKIL
SAKAAVDCSVPVSVSTSIKYADQQRREKLKKELAQCEKEFKLTKTAMRANYKNNSKSLFN
TLQKPSGEPQIEDDMLKEEMNGFSSFARSLVPSSERLHLSLHKSSKVITNGPEKNSSSSP
SSVDYAASGPRKLSSGALYGRRPRSTFPNSHRFQLVISKAPSGDLLDKHSELFSNKQLPF
TPRTLKTEAKSFLSQYRYYTPAKRKKDFTDQRIEAETQTELSFKSELGTAETKNMTDSEM
NIKQASNCVTYDAKEKIAPLPLEGHDSTWDEIKDDALQHSSPRAMCQYSLKPPSTRKIYS
DEEELLYLSFIEDVTDEILKLGLFSNRFLERLFERHIKQNKHLEEEKMRHLLHVLKVDLG
CTSEENSVKQNDVDMLNVFDFEKAGNSEPNELKNESEVTIQQERQQYQKALDMLLSAPKD
ENEIFPSPTEFFMPIYKSKHSEGVIIQQVNDETNLETSTLDENHPSISDSLTDRETSVNV
IEGDSDPEKVEISNGLCGLNTSPSQSVQFSSVKGDNNHDMELSTLKIMEMSIEDCPLDV

Sequence length

599

Interactions

View interactions

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Leber Congenital Amaurosis	Leber congenital amaurosis 3, leber congenital amaurosis	rs386834241, rs767745816, rs777069665, rs75895925, rs567890014, rs878853385, rs371609982, rs2077123571, rs386834243, rs768028061, rs2077123914, rs140287375, rs374268850, rs786204787, rs1555370458, rs80044281, rs753697847 View all (2 more)	N/A
retinal dystrophy	Retinal dystrophy	rs777069665, rs878853385, rs75895925, rs140287375, rs80044281	N/A
Retinitis Pigmentosa	retinitis pigmentosa, Autosomal recessive retinitis pigmentosa	rs374268850, rs767745816	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Attention Deficit Hyperactivity Disorder	Attention deficit hyperactivity disorder	N/A	N/A	GWAS
Glioblastoma	Glioblastoma	N/A	N/A	GWAS

Show/Hide Text Mining Associations (11)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Atrophy	Associate	31908400
Choroidal sclerosis	Associate	29411205
Cone Rod Dystrophies	Associate	26854980
Hypertensive Retinopathy	Associate	31908400
Hypopigmentation	Associate	31908400
Leber Congenital Amaurosis	Associate	18936139, 21602930, 22219627, 25814828, 26147992, 28966547, 31908400, 36140798
Myopia	Associate	31908400
Patterned dystrophy of retinal pigment epithelium	Associate	29411205
Retinal Degeneration	Associate	26854980
Retinal Dystrophies	Associate	25133751, 25814828, 31908400, 33173045, 36140798
Retinitis Pigmentosa	Associate	25814828, 26854980, 29411205, 31908400

SPATA7 (spermatogenesis associated 7)