TTC29 (tetratricopeptide repeat domain 29)

Gene

• Entrez ID: 83894
• Gene name: Tetratricopeptide repeat domain 29
• Gene symbol: TTC29
• Synonyms (NCBI Gene): NYD-SP14, SPGF42, TBPP2A
• Chromosome: 4
• Chromosome location: 4q31.22

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs763399136	G>A,T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, synonymous variant
rs766352190	CCTCC>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1489738488	G>A,C	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, stop gained, synonymous variant
rs1579486914	C>T	Pathogenic	Non coding transcript variant, genic downstream transcript variant, downstream transcript variant, 3 prime UTR variant
rs1579951018	ATTATGTACATCTT>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019129	hsa-miR-335-5p	Microarray	18185580

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003341	Process	Cilium movement	IBA
GO:0003341	Process	Cilium movement	IDA	31735292
GO:0003341	Process	Cilium movement	IMP	31735294
GO:0005737	Component	Cytoplasm	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0031514	Component	Motile cilium	IEA
GO:0036126	Component	Sperm flagellum	IBA
GO:0036126	Component	Sperm flagellum	IDA	31735292, 37934199
GO:0036126	Component	Sperm flagellum	IMP	31735294
GO:0042995	Component	Cell projection	IEA
GO:0044782	Process	Cilium organization	IDA	31735292, 31735294

Other IDs

• MIM: 618735
• HGNC: 29936
• e!Ensembl: ENSG00000137473

Protein

• UniProt ID: Q8NA56
• Protein name: Tetratricopeptide repeat protein 29 (TPR repeat protein 29) (Protein TBPP2A) (Testis development protein NYD-SP14)
• Protein function: Axonemal protein which is implicated in axonemal and/or peri-axonemal structure assembly and regulates flagellum assembly and beating and therefore sperm motility.
• PDB: 8J07
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13424	TPR_12	313 → 383		Repeat

• Tissue specificity: TISSUE SPECIFICITY: Expressed in spermatozoa (at protein level). {ECO:0000269|PubMed:31735292, ECO:0000269|PubMed:31735294}.
• Sequence:

  MTTLPPLPMTRPKLTALARQKLPCSSRKIPRSQLIKEKDDIDHYLEVNFKGLSKEEVAAY
  RNSYKKNICVDMLRDGYHKSFTELFALMERWDALREAARVRSLFWLQKPLEEQPDKLDYL
  YHYLTRAEDAERKESFEDVHNNLYALACYFNNSEDKWVRNHFYERCFKIAQLIKIDCGKK
  EAEAHMHMGLLYEEDGQLLEAAEHYEAFHQLTQGRIWKDETGRSLNLLACESLLRTYRLL
  SDKMLENKEYKQAIKILIKASEIAKEGSDKKMEAEASYYLGLAHLAAEEYETALTVLDTY
  CKISTDLDDDLSLGRGYEAIAKVLQSQGEMTEAIKYLKKFVKIARNNFQSLDLVRASTML
  GDIYNEKGYYNKASECFQQAFDTTVELMSMPLMDETKVHYGIAKAHQMMLTVNNYIESAD
  LTSLNYLLSWKESRGNIEPDPVTEEFRGSTVEAVSQNSERLEELSRFPGDQKNET

• Sequence length: 475

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
Male infertility with spermatogenesis disorder	Likely pathogenic	rs759110348	RCV004018285	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Papillary renal cell carcinoma type 1	Pathogenic	rs1579787268	RCV005912199	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 42	Pathogenic	rs1579486914, rs766352190, rs763399136, rs1489738488, rs1579951018, rs1579787268	RCV000993807 RCV000993808 RCV000993809 RCV000993810 RCV000993811 RCV000993812	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CANNABIS DEPENDENCE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CERVICAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CERVICAL CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL IMPAIRMENT OF SPERMATOZOA MOTILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ 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
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RESTLESS LEGS SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Non-syndromic male infertility due to sperm motility disorder	Non-Syndromic Male Infertility Due To Sperm Motility Disorder	Orphanet			★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	36941558	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	32034058	Associate	★☆☆☆☆ Found in Text Mining only