SPATA7 (spermatogenesis associated 7)

Gene

• Entrez ID: 55812
• Gene name: Spermatogenesis associated 7
• Gene symbol: SPATA7
• Synonyms (NCBI Gene): HEL-S-296, HSD-3.1, HSD3, LCA3, RP94
• 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

SNPs

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

Gene ontology (GO)

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

Other IDs

• MIM: 609868
• HGNC: 20423
• e!Ensembl: 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

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Autosomal recessive retinitis pigmentosa	Likely pathogenic; Pathogenic	rs767745816	RCV001257831	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leber congenital amaurosis 3	Pathogenic; Likely pathogenic	rs1438636453, rs777346333, rs1436269510, rs749304751, rs2140004149, rs2139995462, rs2140004287, rs567890014, rs80044281, rs386834241, rs75895925, rs386834243, rs866837129, rs757972260, rs2504246108, rs786204787, rs767745816, rs2504238331, rs2504079165, rs2504245792, rs2504262624, rs2504237386, rs2504271197, rs2504262571, rs878853385, rs2504297792, rs777506416, rs140287375, rs374268850, rs1555370458, rs753697847, rs777069665, rs2077123571, rs2077123914, rs554224437, rs2077137130, rs1387058171, rs1240995964, rs1227147156, rs2075555029, rs761981554, rs779101498, rs1223558848	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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Melanoma	Pathogenic	rs761981554	RCV005909234	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Likely pathogenic; Pathogenic	rs80044281, rs75895925, rs2504262571, rs878853385, rs1595270842, rs140287375, rs777069665, rs761981554	RCV004814791 RCV003887848 RCV004817167 RCV000225504 RCV003889658 RCV001075501 RCV001075549 RCV003887976	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs767745816, rs374268850	RCV001003226 RCV002466542	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa 94, variable age at onset	Likely pathogenic; Pathogenic	rs75895925, rs386834243, rs140287375, rs753697847, rs777069665	RCV002260581 RCV002260582 RCV002260600 RCV002264714 RCV002264742	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SPATA7-related disorder	Likely pathogenic; Pathogenic	rs80044281, rs140287375, rs777069665	RCV000358776 RCV000778417 RCV000778418	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Papillary renal cell carcinoma type 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA, JUVENILE, SPATA7-RELATED	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STARGARDT DISEASE 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amaurosis congenita of Leber, type 1	Leber congenital amaurosis	BEFREE	20104588, 21310915, 21602930, 22219627, 29100828, 9799089		★☆☆☆☆ Found in Text Mining only
Atrophy	Atrophy	Pubtator	31908400	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	18723074		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Choroidal sclerosis	Choroidal sclerosis	Pubtator	29411205	Associate	★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophies	Cone-rod dystrophy	BEFREE	26854980		★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophy 2	Cone-rod dystrophy	BEFREE	26854980		★☆☆☆☆ Found in Text Mining only
Congenital Amaurosis of Retinal Origin	Dysgenesis Neuroepithelialis Retinae	CTD_human_DG	19268277		★☆☆☆☆ Found in Text Mining only
Congenital cerebral hernia	Congenital Cerebral Hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hemiplegia/hemiparesis	Hemiplegia/hemiparesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrophy of clitoris	Hypertrophy Of Clitoris	BEFREE	25894637		★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Leber Congenital Amaurosis	Leber Congenital Amaurosis	BEFREE	16269441, 19268277, 20104588, 21310915, 22219627, 25814828, 29100828		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leber Congenital Amaurosis	Leber congenital amaurosis	Pubtator	18936139, 21602930, 22219627, 25814828, 26147992, 28966547, 31908400, 36140798	Associate	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leber Congenital Amaurosis	Leber Congenital Amaurosis	CTD_human_DG	19268277		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leber Congenital Amaurosis	Leber Congenital Amaurosis	ORPHANET_DG	19268277, 25685757		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leber congenital amaurosis	Leber Congenital Amaurosis	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leber Congenital Amaurosis	Leber Congenital Amaurosis	GENOMICS_ENGLAND_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
LEBER CONGENITAL AMAUROSIS 3 (disorder)	Leber Congenital Amaurosis	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
LEBER CONGENITAL AMAUROSIS 3 (disorder)	Leber Congenital Amaurosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Male Pseudohermaphroditism	Male Pseudohermaphroditism	BEFREE	9758445		★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	31908400	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Patterned dystrophy of retinal pigment epithelium	Patterned macular dystrophy	Pubtator	29411205	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Degeneration	Retinal degeneration	Pubtator	26854980	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Dystrophy, Early Onset Severe	Retinal Dystrophy	ORPHANET_DG	21310915		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	19268277, 20104588, 25814828, 26854980, 29100828		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	ORPHANET_DG	19268277		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	CTD_human_DG	19268277		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa	Retinitis Pigmentosa	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	25814828, 26854980, 29411205, 31908400	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa, Juvenile, SPATA7-Related	Retinitis Pigmentosa	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Rod-Cone Dystrophy	Rod-cone dystrophy	BEFREE	20104588, 26854980		★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Severe early-childhood-onset retinal dystrophy	Retinal Dystrophy	Orphanet			★☆☆☆☆ Found in Text Mining only