TDRD7 (tudor domain containing 7)

Gene

• Entrez ID: 23424
• Gene name: Tudor domain containing 7
• Gene symbol: TDRD7
• Synonyms (NCBI Gene): CATC4, PCTAIRE2BP, TRAP
• Chromosome: 9
• Chromosome location: 9q22.33
• Summary: The protein encoded by this gene belongs to the Tudor family of proteins. This protein contains conserved Tudor domains and LOTUS domains. It is a component of RNA granules, which function in RNA processing. Mutations in this gene have been associated wit

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs765628635	G>-	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs1477743112	G>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1554743428	->A	Pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1554744860	->A	Pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT030170	hsa-miR-26b-5p	Microarray	19088304
MIRT051693	hsa-let-7e-5p	CLASH	23622248
MIRT2461291	hsa-miR-4803	CLIP-seq
MIRT2640488	hsa-miR-3161	CLIP-seq
MIRT2640489	hsa-miR-576-5p	CLIP-seq
MIRT2640488	hsa-miR-3161	CLIP-seq
MIRT2640489	hsa-miR-576-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002089	Process	Lens morphogenesis in camera-type eye	IBA
GO:0002089	Process	Lens morphogenesis in camera-type eye	IEA
GO:0002089	Process	Lens morphogenesis in camera-type eye	IMP	21436445
GO:0003723	Function	RNA binding	IEA
GO:0003729	Function	MRNA binding	IDA	21436445
GO:0005515	Function	Protein binding	IPI	14603251, 16189514, 21988832, 25416956, 33961781
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0007283	Process	Spermatogenesis	IBA
GO:0007283	Process	Spermatogenesis	IEA
GO:0007283	Process	Spermatogenesis	ISS
GO:0010608	Process	Post-transcriptional regulation of gene expression	IMP	21436445
GO:0030154	Process	Cell differentiation	IEA
GO:0030719	Process	P granule organization	IBA
GO:0033391	Component	Chromatoid body	ISS
GO:0034587	Process	PiRNA processing	IBA
GO:0035770	Component	Ribonucleoprotein granule	IDA	21436445
GO:0035770	Component	Ribonucleoprotein granule	IEA
GO:0043186	Component	P granule	IBA
GO:0070306	Process	Lens fiber cell differentiation	IBA
GO:0070306	Process	Lens fiber cell differentiation	IEA
GO:0070306	Process	Lens fiber cell differentiation	IMP	21436445

Other IDs

• MIM: 611258
• HGNC: 30831
• e!Ensembl: ENSG00000196116

Protein

• UniProt ID: Q8NHU6
• Protein name: Tudor domain-containing protein 7 (PCTAIRE2-binding protein) (Tudor repeat associator with PCTAIRE-2) (Trap)
• Protein function: Component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. Required for lens transparency during lens development, by
• PDB: 3RCO
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12872	OST-HTH	5 → 72	OST-HTH/LOTUS domain	Domain
  PF12872	OST-HTH	233 → 277	OST-HTH/LOTUS domain	Domain
  PF00567	TUDOR	459 → 581	Tudor domain	Domain
  PF00567	TUDOR	648 → 775	Tudor domain	Domain
  PF00567	TUDOR	908 → 1026	Tudor domain	Domain

• Sequence:

  MLEGDLVSKMLRAVLQSHKNGVALPRLQGEYRSLTGDWIPFKQLGFPTLEAYLRSVPAVV
  RIETSRSGEITCYAMACTETARIAQLVARQRSSKRKTGRQVNCQMRVKKTMPFFLEGKPK
  ATLRQPGFASNFSVGKKPNPAPLRDKGNSVGVKPDAEMSPYMLHTTLGNEAFKDIPVQRH
  VTMSTNNRFSPKASLQPPLQMHLSRTSTKEMSDNLNQTVEKPNVKPPASYTYKMDEVQNR
  IKEILNKHNNGIWISKLPHFYKELYKEDLNQGILQQFEHWPHICTVEKPCSGGQDLLLYP
  AKRKQLLRSELDTEKVPLSPLPGPKQTPPLKGCPTVMAGDFKEKVADLLVKYTSGLWASA
  LPKAFEEMYKVKFPEDALKNLASLSDVCSIDYISGNPQKAILYAKLPLPTDKIQKDAGQA
  HGDNDIKAMVEQEYLQVEESIAESANTFMEDITVPPLMIPTEASPSVLVVELSNTNEVVI
  RYVGKDYSAAQELMEDEMKEYYSKNPKITPVQAVNVGQLLAVNAEEDAWLRAQVISTEEN
  KIKVCYVDYGFSENVEKSKAYKLNPKFCSLSFQATKCKLAGLEVLSDDPDLVKVVESLTC
  GKIFAVEILDKADIPLVVLYDTSGEDDININATCLKAICDKSLEVHLQVDAMYTNVKVTN
  ICSDGTLYCQVPCKGLNKLSDLLRKIEDYFHCKHMTSECFVSLPFCGKICLFHCKGKWLR
  VEITNVHSSRALDVQFLDSGTVTSVKVSELREIPPRFLQEMIAIPPQAIKCCLADLPQSI
  GMWTPDAVLWLRDSVLNCSDCSIKVTKVDETRGIAHVYLFTPKNFPDPHRSINRQITNAD
  LWKHQKDVFLSAISSGADSPNSKNGNMPMSGNTGENFRKNLTDVIKKSMVDHTSAFSTEE
  LPPPVHLSKPGEHMDVYVPVACHPGYFVIQPWQEIHKLEVLMEEMILYYSVSEERHIAVE
  KDQVYAAKVENKWHRVLLKGILTNGLVSVYELDYGKHELVNIRKVQPLVDMFRKLPFQAV
  TAQLAGVKCNQWSEEASMVFRNHVEKKPLVALVQTVIENANPWDRKVVVYLVDTSLPDTD
  TWIHDFMSEYLIELSKVN

• Sequence length: 1098

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
Cataract 36	Pathogenic; Likely pathogenic	rs2131165749, rs2490721602, rs748412471, rs750207077, rs765628635, rs1554744860, rs1554743428, rs1477743112	RCV001614464 RCV003318472 RCV003234833 RCV000023890 RCV000488876 RCV000656384 RCV000656385 RCV000985207	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATYPICAL FEMORAL FRACTURE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CATARACT	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL CATARACT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental cataract	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFERTILITY, MALE	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALE INFERTILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TDRD7-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Carcinoma Renal Cell	Stimulate	35273654	★☆☆☆☆ Found in Text Mining only
Cataract	Associate	25120344, 33339270, 33923544	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract Age Related Nuclear	Associate	24435515	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	32828126, 34080453, 34169901	★☆☆☆☆ Found in Text Mining only
Genetic Diseases Inborn	Associate	28418495	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	35273654	★☆☆☆☆ Found in Text Mining only