TDRD9 (tudor domain containing 9)

Gene

• Entrez ID: 122402
• Gene name: Tudor domain containing 9
• Gene symbol: TDRD9
• Synonyms (NCBI Gene): C14orf75, HIG-1, HLS, NET54, SPGF30, SPNE
• Chromosome: 14
• Chromosome location: 14q32.33

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs765353898	TAGT>-	Pathogenic	Genic upstream transcript variant, 5 prime UTR variant, frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1417159	hsa-miR-1287	CLIP-seq
MIRT1417160	hsa-miR-1912	CLIP-seq
MIRT1417161	hsa-miR-194	CLIP-seq
MIRT1417162	hsa-miR-3125	CLIP-seq
MIRT1417163	hsa-miR-3135b	CLIP-seq
MIRT1417164	hsa-miR-3138	CLIP-seq
MIRT1417165	hsa-miR-3591-3p	CLIP-seq
MIRT1417166	hsa-miR-3612	CLIP-seq
MIRT1417167	hsa-miR-3916	CLIP-seq
MIRT1417168	hsa-miR-4443	CLIP-seq
MIRT1417169	hsa-miR-4455	CLIP-seq
MIRT1417170	hsa-miR-4494	CLIP-seq
MIRT1417171	hsa-miR-4717-5p	CLIP-seq
MIRT1417172	hsa-miR-4800-5p	CLIP-seq
MIRT1417173	hsa-miR-650	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	IBA
GO:0003724	Function	RNA helicase activity	IEA
GO:0004386	Function	Helicase activity	IBA
GO:0004386	Function	Helicase activity	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	28536242
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	28536242
GO:0005737	Component	Cytoplasm	IEA
GO:0007140	Process	Male meiotic nuclear division	IEA
GO:0007140	Process	Male meiotic nuclear division	ISS
GO:0007141	Process	Male meiosis I	IEA
GO:0007141	Process	Male meiosis I	ISS
GO:0007283	Process	Spermatogenesis	IEA
GO:0007283	Process	Spermatogenesis	IMP	28536242
GO:0007283	Process	Spermatogenesis	ISS
GO:0009566	Process	Fertilization	IEA
GO:0009566	Process	Fertilization	ISS
GO:0010526	Process	Transposable element silencing	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0016887	Function	ATP hydrolysis activity	ISS
GO:0030154	Process	Cell differentiation	IEA
GO:0031047	Process	Regulatory ncRNA-mediated gene silencing	IEA
GO:0034587	Process	PiRNA processing	IEA
GO:0034587	Process	PiRNA processing	ISS
GO:0051321	Process	Meiotic cell cycle	IEA
GO:0071547	Component	PiP-body	IEA
GO:0071547	Component	PiP-body	ISS
GO:0141006	Process	Transposable element silencing by piRNA-mediated heterochromatin formation	IEA
GO:0141006	Process	Transposable element silencing by piRNA-mediated heterochromatin formation	ISS
GO:0141196	Process	Transposable element silencing by piRNA-mediated DNA methylation	IEA
GO:0141196	Process	Transposable element silencing by piRNA-mediated DNA methylation	ISS

Other IDs

• MIM: 617963
• HGNC: 20122
• e!Ensembl: ENSG00000156414

Protein

• UniProt ID: Q8NDG6
• Protein name: ATP-dependent RNA helicase TDRD9 (EC 3.6.4.13) (Tudor domain-containing protein 9)
• Protein function: ATP-binding RNA helicase required during spermatogenesis (PubMed:28536242). Required to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which medi
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00270	DEAD	135 → 298	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	376 → 501	Helicase conserved C-terminal domain	Family
  PF04408	HA2	565 → 702	Helicase associated domain (HA2)	Domain
  PF00567	TUDOR	899 → 1015	Tudor domain	Domain

• Sequence:

  MLRKLTIEQINDWFTIGKTVTNVELLGAPPAFPAGAAREEVQRQDVAPGAGPAAQAPALA
  QAPARPAAAFERSLSQRSSEVEYINKYRQLEAQELDVCRSVQPTSGPGPRPSLAKLSSVT
  CIPGTTYKYPDLPISRYKEEVVSLIESNSVVIIHGATGSGKSTQLPQYILDHYVQRSAYC
  SIVVTQPRKIGASSIARWISKERAWTLGGVVGYQVGLEKIATEDTRLIYMTTGVLLQKIV
  SAKSLMEFTHIIIDEVHERTEEMDFLLLVVRKLLRTNSRFVKVVLMSATISCKEFADYFA
  VPVQNKMNPAYIFEVEGKPHSVEEYYLNDLEHIHHSKLSPHLLEEPVITKDIYEVAVSLI
  QMFDDLDMKESGNKAWSGAQFVLERSSVLVFLPGLGEINYMHELLTSLVHKRLQVYPLHS
  SVALEEQNNVFLSPVPGYRKIILSTNIAESSVTVPDVKYVIDFCLTRTLVCDEDTNYQSL
  RLSWASKTSCNQRKGRAGRVSRGYCYRLVHKDFWDNSIPDHVVPEMLRCPLGSTILKVKL
  LDMGEPRALLATALSPPGLSDIERTILLLKEVGALAVSGQREDENPHDGELTFLGRVLAQ
  LPVNQQLGKLIVLGHVFGCLDECLIIAAALSLKNFFAMPFRQHLDGYRNKVNFSGSSKSD
  CIALVEAFKTWKACRQTGELRYPKDELNWGRLNYIQIKRIREVAELYEELKTRISQFNMH
  VDSRRPVMDQEYIYKQRFILQVVLAGAFYPNYFTFGQPDEEMAVRELAGKDPKTTVVLKH
  IPPYGFLYYKQLQSLFRQCGQVKSIVFDGAKAFVEFSRNPTERFKTLPAVYMAIKMSQLK
  VSLELSVHSAEEIEGKVQGMNVSKLRNTRVNVDFQKQTVDPMQVSFNTSDRSQTVTDLLL
  TIDVTEVVEVGHFWGYRIDENNSEILKKLTAEINQLTLVPLPTHPHPDLVCLAPFADFDK
  QRYFRAQVLYVSGNSAEVFFVDYGNKSHVDLHLLMEIPCQFLELPFQALEFKICKMRPSA
  KSLVCGKHWSDGASQWFASLVSGCTLLVKVFSVVHSVLHVDVYQYSGVQDAINIRDVLIQ
  QGYAELTEESYESKQSHEVLKGLFSKSVENMTDGSVPFPMKDDEKYLIRILLESFSTNKL
  GTPNCKAELHGPFNPYELKCHSLTRISKFRCVWIEKESINSVIISDAPEDLHQRMLVAAS
  LSINATGSTMLLRETSLMPHIPGLPALLSMLFAPVIELRIDQNGKYYTGVLCGLGWNPAT
  GASILPEHDMELAFDVQFSVEDVVEVNILRAAINKLVCDGPNGCKCLGPERVAQLQDIAR
  QKLLGLFCQSKPREKIVPKWHEKPYEWNQVDPKLVMEQADRESSRGKNTFLYQLHKLVVL
  GT

• Sequence length: 1382

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
Azoospermia	Pathogenic	rs2152252501, rs765353898	RCV001797573 RCV001797124	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Male infertility	Likely pathogenic	rs748634340, rs773919914	RCV004573398 RCV004573399	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 30	Likely pathogenic; Pathogenic	rs777065614, rs765353898	RCV004566422 RCV000678505	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALE INFERTILITY WITH AZOOSPERMIA OR OLIGOZOOSPERMIA DUE TO SINGLE GENE MUTATION	—	Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSYCHIATRIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TDRD9-related disorder	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	29515758		★☆☆☆☆ Found in Text Mining only
Adrenal Gland Pheochromocytoma	Adrenal Gland Pheochromocytoma	BEFREE	1673491		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	31395040		★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	30482079		★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	30482079		★☆☆☆☆ Found in Text Mining only
Azoospermia	Azoospermia	BEFREE	22223142		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Azoospermia	Azoospermia	Pubtator	35172124	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Azoospermia	Azoospermia	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Azoospermia, Nonobstructive	Azoospermia	BEFREE	27233649		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	28221213		★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	29515758		★☆☆☆☆ Found in Text Mining only
Cerebral Palsy	Cerebral palsy	BEFREE	31305380		★☆☆☆☆ Found in Text Mining only
Color Blindness, Blue	Color blindness	BEFREE	28403472		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	38137029	Associate	★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	30902699		★☆☆☆☆ Found in Text Mining only
Male infertility with azoospermia or oligozoospermia due to single gene mutation	Male infertility	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of breast	Breast Cancer	BEFREE	28221213		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30998604		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	1431953		★☆☆☆☆ Found in Text Mining only
Non-obstructive azoospermia	Non-obstructive azoospermia	BEFREE	28536242		★☆☆☆☆ Found in Text Mining only
Non-obstructive azoospermia	Non-obstructive azoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obstructive azoospermia	Obstructive azoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pheochromocytoma	Pheochromocytoma	BEFREE	1673491		★☆☆☆☆ Found in Text Mining only
Retinal Vein Occlusion	Retinal Vein Occlusion	BEFREE	31395040		★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	36211409	Associate	★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasms	Thyroid cancer	Pubtator	33711033	Associate	★☆☆☆☆ Found in Text Mining only
Von Hippel-Lindau Syndrome	Von Hippel-Lindau Syndrome	BEFREE	1673491		★☆☆☆☆ Found in Text Mining only