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
Disease Acronyms (UniProt) Disease acronyms from UniProt database	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(21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000226	Process	Microtubule cytoskeleton organization	IBA	21873635
GO:0005515	Function	Protein binding	IPI	25398945
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005930	Component	Axoneme	IBA	21873635
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	ISS
GO:0036064	Component	Ciliary basal body	IBA	21873635
GO:0036064	Component	Ciliary basal body	IDA	25398945
GO:0045494	Process	Photoreceptor cell maintenance	IBA	21873635
GO:0045494	Process	Photoreceptor cell maintenance	ISS
GO:0050896	Process	Response to stimulus	IEA
GO:0120200	Component	Rod photoreceptor outer segment	IBA	21873635
GO:0120206	Component	Photoreceptor distal connecting cilium	IBA	21873635
GO:1903546	Process	Protein localization to photoreceptor outer segment	IBA	21873635
GO:1903546	Process	Protein localization to photoreceptor outer segment	ISS
GO:1903621	Process	Protein localization to photoreceptor connecting cilium	IBA	21873635
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 (14)

Disease term	Disease name	dbSNP ID	References
Causal
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322 View all (150 more)
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Diabetes mellitus	Diabetes Mellitus, Non-Insulin-Dependent	rs587776515, rs61730328, rs606231121, rs606231122, rs79020217, rs77625743, rs78378398, rs606231123, rs1362648752, rs104893649, rs80356624, rs80356616, rs80356625, rs80356611, rs104894237 View all (293 more)
Glaucoma	Glaucoma	rs121918355, rs1566660365, rs1566635134, rs121918356, rs1566634475, rs28936700, rs55771538, rs28936701, rs104893622, rs55989760, rs72549387, rs104893628, rs2125316417, rs104893629, rs74315328 View all (29 more)
Hearing loss	Conductive hearing loss, Sensorineural Hearing Loss (disorder)	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359 View all (184 more)
Hyperinsulinism	Hyperinsulinism	rs387906407, rs151344623, rs121913156, rs137853245, rs80356655, rs104894010, rs104894012, rs104894014, rs104894015, rs137852676, rs587783169, rs72559716, rs541269678, rs151344624, rs797045209 View all (23 more)
Keratoconus	Keratoconus	rs273585637, rs273585632, rs273585616, rs273585618, rs281865144, rs281865150, rs1553500862, rs756938019
Leber congenital amaurosis	Leber Congenital Amaurosis, LEBER CONGENITAL AMAUROSIS 3 (disorder), Leber congenital amaurosis	rs386834252, rs386834253, rs121918165, rs62635288, rs281865192, rs137852833, rs137852834, rs137852835, rs2137919146, rs267606719, rs80044281, rs386834241, rs75895925, rs386834243, rs750962965 View all (532 more)	19268277, 25685757
Mental retardation	Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Obesity	Obesity	rs74315349, rs1474810899, rs121918111, rs796065034, rs753856820, rs796065035, rs121918112, rs104894023, rs137852821, rs1580764441, rs137852822, rs137852823, rs137852824, rs13447324, rs121913562 View all (27 more)
Optic atrophy	Optic Atrophy	rs121434508, rs267607017, rs80356524, rs80356525, rs879255560, rs104893753, rs80356529, rs397515360, rs104893620, rs199476104, rs199476112, rs199476118, rs398124298, rs770066665, rs398124299 View all (37 more)
Retinal dystrophy	Retinal Dystrophy, Early Onset Severe, Severe early-childhood-onset retinal dystrophy	rs267606794, rs200691042, rs397704718, rs202193201, rs794728002, rs121965036, rs121965057, rs121918129, rs137853190, rs386834252, rs121918165, rs137853113, rs137853114, rs121918328, rs587777803 View all (2328 more)	21310915
Retinitis pigmentosa	Retinitis Pigmentosa, Retinitis Pigmentosa, Juvenile, SPATA7-Related, Retinitis pigmentosa	rs267606794, rs200691042, rs397704718, rs202193201, rs267606793, rs2147483647, rs779886453, rs267606691, rs794728002, rs878853253, rs137853189, rs137853190, rs137853112, rs137853113, rs137853114 View all (1830 more)	19268277

Show/Hide Unknown Diseases (5)

Disease term	Disease name	Evidence	Source
Unknown
Leber Congenital Amaurosis	Leber congenital amaurosis 3, Leber congenital amaurosis		GenCC
Retinitis Pigmentosa	retinitis pigmentosa		GenCC
Retinal Dystrophy	severe early-childhood-onset retinal dystrophy		GenCC
Attention Deficit Hyperactivity Disorder	Attention Deficit Hyperactivity Disorder		GWAS
Glioblastoma	Glioblastoma	CRISPR screening of E3 ubiquitin ligases reveals Ring Finger Protein 185 as a novel tumor suppressor in glioblastoma repressed by promoter hypermethylation and miR-587	GWAS, CBGDA

Show/Hide Text Mining Associations (11)

Disease Name	Relationship Type	References
Associations from Text Mining
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)