TMEM260 (transmembrane protein 260)

Gene

• Entrez ID: 54916
• Gene name: Transmembrane protein 260
• Gene symbol: TMEM260
• Synonyms (NCBI Gene): C14orf101, SHDRA
• Chromosome: 14
• Chromosome location: 14q22.3

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs201956469	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, intron variant
rs568247949	AAGAA>-	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004169	Function	Dolichyl-phosphate-mannose-protein mannosyltransferase activity	IDA	37186866
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	37186866
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IEA
GO:0051604	Process	Protein maturation	IDA	37186866

Other IDs

• MIM: 617449
• HGNC: 20185
• e!Ensembl: ENSG00000070269

Protein

• UniProt ID: Q9NX78
• Protein name: Protein O-mannosyl-transferase TMEM260 (EC 2.4.1.109) (Transmembrane protein 260)
• Protein function: O-mannosyl-transferase that transfers mannosyl residues to the hydroxyl group of serine or threonine residues of proteins (PubMed:37186866). Specifically glycosylates the IPT/TIG domain of target proteins, such as MET and MST1R/RON (PubMed:37186
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF11028	DUF2723	52 → 215	Protein of unknown function (DUF2723)	Family

• Tissue specificity: TISSUE SPECIFICITY: [Isoform 1]: Expressed in brain, heart, kidney, liver, lung, pancreas and placenta but are not detected in skeletal muscle. {ECO:0000269|PubMed:28318500}.; TISSUE SPECIFICITY: [Isoform 3]: Expressed in brain, heart, kidney, liver, lung
• Sequence:

  MSPHGDGRGQAQGRAVRVGLRRSGGIRGGVAVFAAVAAVFTFTLPPSVPGGDSGELITAA
  HELGVAHPPGYPLFTLVAKLAITLFPFGSIAYRVNLLCGLFGAVAASLLFFTVFRLSGSS
  AGGILAAGVFSFSRLTWQWSIAAEVFSLNNLFVGLLMALTVHFEEAATAKERSKVAKIGA
  FCCGLSLCNQHTIILYVLCIIPWILFQLLKKKELSLGSLLKLSLYFSAGLLPYVHLPISS
  YLNHARWTWGDQTTLQGFLTHFLREEYGTFSLAKSEIGSSMSEILLSQVTNMRTELSFNI
  QALAVCANICLATKDRQNPSLVWLFTGMFCIYSLFFAWRANLDISKPLFMGVVERFWMQS
  NAVVAVLAGIGLAAVVSETNRVLNSNGLQCLEWLSATLFVVYQIYSNYSVCDQRTNYVID
  KFAKNLLTSMPHDAIILLRGDLPGNSLRYMHYCEGLRPDISLVDQEMMTYEWYLPKMAKH
  LPGVNFPGNRWNPVEGILPSGMVTFNLYHFLEVNKQKETFVCIGIHEGDPTWKKNYSLWP
  WGSCDKLVPLEIVFNPEEWIKLTKSIYNWTEEYGRFDPSSWESVANEEMWQARMKTPFFI
  FNLAETAHMPSKVKAQLYAQAYDLYKEIVYLQKEHPVNWHKNYAIACERMLRLQARDADP
  EVLLSETIRHFRLYSQKAPNDPQQADILGALKHLRKELQSLRNRKNV

• Sequence length: 707

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
Structural heart defects and renal anomalies syndrome	Pathogenic; Likely pathogenic	rs1885455089, rs761443112, rs141599092, rs1351329464, rs747632686, rs2139626950, rs2503654780, rs2503562017, rs375476463, rs2503448012, rs1353172878, rs1566561439, rs2503604772, rs766333701, rs201956469, rs1085307449, rs1888745759, rs773888234	RCV001568326 RCV001568327 RCV001568351 RCV001775180 RCV001775195 RCV001783876 RCV002470246 RCV002776549 RCV002814355 RCV003333641 RCV003990394 RCV004527556 RCV004579648 RCV004586402 RCV000488880 RCV000488879 RCV001251161 RCV005253782	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Type I truncus arteriosus	Pathogenic	rs1351329464	RCV001845027	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
TETRALOGY OF FALLOT	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TMEM260-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 1 TRUNCUS ARTERIOSUS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Heart Defects Congenital	Congenital heart defect	Pubtator	38351237	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Lymphoma, Non-Hodgkin	Non-Hodgkin lymphoma	BEFREE	24831772		★☆☆☆☆ Found in Text Mining only
Lymphoma, Non-Hodgkin, Familial	Lymphoma	BEFREE	24831772		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24831772		★☆☆☆☆ Found in Text Mining only
Microvascular Angina	Microvascular angina	Pubtator	28318500	Associate	★☆☆☆☆ Found in Text Mining only
Partial agenesis of corpus callosum	Partial Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Renal Insufficiency	Renal Insufficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
STRUCTURAL HEART DEFECTS AND RENAL ANOMALIES SYNDROME	Structural Heart Defects And Renal Anomalies Syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Truncus Arteriosus, Persistent	Persistent truncus arteriosus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only