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

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Associated diseases
Entrez ID	55812
Gene name	Spermatogenesis associated 7
Gene symbol	SPATA7
Synonyms (NCBI Gene)	HEL-S-296HSD-3.1HSD3LCA3RP94
Chromosome	14
Chromosome location	14q31.3
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 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

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

563

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive retinitis pigmentosa	Likely pathogenic; Pathogenic	rs767745816	RCV001257831
Leber congenital amaurosis	Pathogenic; Likely pathogenic	rs777346333, rs80044281, rs75895925, rs2077134911, rs200244203, rs767745816, rs1472791220, rs2076489265, rs777598239, rs371609982, rs768028061, rs777069665, rs567890014	RCV001844288 RCV003987304 RCV003485517 RCV002266502 RCV002282912 RCV005237635 RCV003155610 RCV003155666 RCV003324679 RCV000515718 RCV000515659 RCV003226389 RCV003324536
Leber congenital amaurosis 3	Pathogenic; Likely pathogenic	rs1438636453, rs777346333, rs1436269510, rs749304751, rs2140004149, rs2139995462, rs2140004287, rs567890014, rs80044281, rs386834241, rs75895925, rs386834243, rs866837129, rs757972260, rs2504246108 View all (28 more)	RCV005214291 RCV001390411 RCV001390780 RCV001384811 RCV001591872 RCV002007252 RCV001920693 RCV001949564 RCV000001460 RCV000001461 RCV000001462 RCV000001463 RCV002246739 RCV002302856 RCV002465073 RCV000169677 RCV001852064 RCV002727117 RCV002819785 RCV002861629 RCV002862958 RCV003014665 RCV003005784 RCV003021020 RCV001383050 RCV003805436 RCV003801888 RCV000023791 RCV000678631 RCV002530977 RCV001860227 RCV001381852 RCV001593160 RCV001059869 RCV001063347 RCV001211404 RCV001243408 RCV001255916 RCV001255918 RCV001255920 RCV001255921 RCV001255917 RCV001255919 RCV005253774
Melanoma	Pathogenic	rs761981554	RCV005909234
Retinal dystrophy	Likely pathogenic; Pathogenic	rs80044281, rs75895925, rs2504262571, rs878853385, rs1595270842, rs140287375, rs777069665, rs761981554	RCV004814791 RCV003887848 RCV004817167 RCV000225504 RCV003889658 RCV001075501 RCV001075549 RCV003887976
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs767745816, rs374268850	RCV001003226 RCV002466542
Retinitis pigmentosa 94, variable age at onset	Likely pathogenic; Pathogenic	rs75895925, rs386834243, rs140287375, rs753697847, rs777069665	RCV002260581 RCV002260582 RCV002260600 RCV002264714 RCV002264742
SPATA7-related disorder	Likely pathogenic; Pathogenic	rs80044281, rs140287375, rs777069665	RCV000358776 RCV000778417 RCV000778418

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs2076986530, rs2076796929	-
Acute myeloid leukemia	Benign	rs60770744	RCV005893301
Cervical cancer	Benign	rs60770744	RCV005893303
Cholangiocarcinoma	Benign	rs75595762	RCV005909712
Colorectal cancer	Conflicting classifications of pathogenicity	rs375371982	RCV005888464
Gastric cancer	Conflicting classifications of pathogenicity; Benign	rs527236050, rs60770744	RCV005867921 RCV005893305
Hepatocellular carcinoma	Benign; Conflicting classifications of pathogenicity	rs386579, rs527236050	RCV005922635 RCV005867920
Lung cancer	Benign	rs60770744	RCV005893307
Malignant tumor of esophagus	Benign	rs60770744	RCV005893302
Optic atrophy	Uncertain significance	rs545998461	RCV004813827
Papillary renal cell carcinoma type 1	Uncertain significance	rs2140009228	RCV005920732
Sarcoma	Benign	rs60770744	RCV005893304
Thymoma	Benign	rs75595762, rs60770744	RCV005909711 RCV005893306
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs375371982	RCV005888465
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	rs60770744, rs142122029	RCV005893308 RCV005898659

Show/Hide Text Mining Associations (11)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)