TMEM165 (transmembrane protein 165)

Gene

• Entrez ID: 55858
• Gene name: Transmembrane protein 165
• Gene symbol: TMEM165
• Synonyms (NCBI Gene): CDG2K, FT27, GDT1, SLC64A1, TMPT27, TPARL
• Chromosome: 4
• Chromosome location: 4q12
• Summary: This gene encodes a predicted transmembrane protein with a perinuclear Golgi-like distribution in fibroblasts. Mutations in this gene are associated with the autosomal recessive disorder congenital disorder of glycosylation, type IIk. Knockdown of this ge

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs387907221	G>A	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs793888506	G>A	Pathogenic	Intron variant
rs886037631	G>A	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs1560383746	C>T	Likely-pathogenic	5 prime UTR variant, stop gained, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT028789	hsa-miR-26b-5p	Microarray	19088304
MIRT052436	hsa-let-7a-5p	CLASH	23622248
MIRT051768	hsa-let-7c-5p	CLASH	23622248
MIRT050801	hsa-miR-17-5p	CLASH	23622248
MIRT039158	hsa-miR-769-5p	CLASH	23622248
MIRT1432062	hsa-miR-101	CLIP-seq
MIRT1432063	hsa-miR-1227	CLIP-seq
MIRT1432064	hsa-miR-1283	CLIP-seq
MIRT1432065	hsa-miR-1298	CLIP-seq
MIRT1432066	hsa-miR-1324	CLIP-seq
MIRT1432067	hsa-miR-144	CLIP-seq
MIRT1432068	hsa-miR-148a	CLIP-seq
MIRT1432069	hsa-miR-148b	CLIP-seq
MIRT1432070	hsa-miR-152	CLIP-seq
MIRT1432071	hsa-miR-2054	CLIP-seq
MIRT1432072	hsa-miR-221	CLIP-seq
MIRT1432073	hsa-miR-222	CLIP-seq
MIRT1432074	hsa-miR-2355-5p	CLIP-seq
MIRT1432075	hsa-miR-30a	CLIP-seq
MIRT1432076	hsa-miR-30b	CLIP-seq
MIRT1432077	hsa-miR-30c	CLIP-seq
MIRT1432078	hsa-miR-30d	CLIP-seq
MIRT1432079	hsa-miR-30e	CLIP-seq
MIRT1432080	hsa-miR-3120-3p	CLIP-seq
MIRT1432081	hsa-miR-3124-3p	CLIP-seq
MIRT1432082	hsa-miR-3166	CLIP-seq
MIRT1432083	hsa-miR-3661	CLIP-seq
MIRT1432084	hsa-miR-3679-3p	CLIP-seq
MIRT1432085	hsa-miR-3942-5p	CLIP-seq
MIRT1432086	hsa-miR-410	CLIP-seq
MIRT1432087	hsa-miR-4277	CLIP-seq
MIRT1432088	hsa-miR-4477b	CLIP-seq
MIRT1432089	hsa-miR-4659a-5p	CLIP-seq
MIRT1432090	hsa-miR-4659b-5p	CLIP-seq
MIRT1432091	hsa-miR-4703-5p	CLIP-seq
MIRT1432092	hsa-miR-4704-5p	CLIP-seq
MIRT1432093	hsa-miR-4716-5p	CLIP-seq
MIRT1432094	hsa-miR-4719	CLIP-seq
MIRT1432095	hsa-miR-4760-3p	CLIP-seq
MIRT1432096	hsa-miR-487a	CLIP-seq
MIRT1432097	hsa-miR-548ae	CLIP-seq
MIRT1432098	hsa-miR-548ag	CLIP-seq
MIRT1432099	hsa-miR-548ai	CLIP-seq
MIRT1432100	hsa-miR-548aj	CLIP-seq
MIRT1432101	hsa-miR-548am	CLIP-seq
MIRT1432102	hsa-miR-548v	CLIP-seq
MIRT1432103	hsa-miR-548x	CLIP-seq
MIRT1432104	hsa-miR-578	CLIP-seq
MIRT1432105	hsa-miR-587	CLIP-seq
MIRT1432106	hsa-miR-631	CLIP-seq
MIRT1432107	hsa-miR-664	CLIP-seq
MIRT1432068	hsa-miR-148a	CLIP-seq
MIRT1432069	hsa-miR-148b	CLIP-seq
MIRT1432070	hsa-miR-152	CLIP-seq
MIRT1554893	hsa-miR-3647-3p	CLIP-seq
MIRT1554894	hsa-miR-3936	CLIP-seq
MIRT1554895	hsa-miR-4697-3p	CLIP-seq
MIRT1554896	hsa-miR-4766-5p	CLIP-seq
MIRT1554897	hsa-miR-512-3p	CLIP-seq
MIRT1432065	hsa-miR-1298	CLIP-seq
MIRT2129515	hsa-miR-200b	CLIP-seq
MIRT2129516	hsa-miR-200c	CLIP-seq
MIRT1432071	hsa-miR-2054	CLIP-seq
MIRT1432074	hsa-miR-2355-5p	CLIP-seq
MIRT1432081	hsa-miR-3124-3p	CLIP-seq
MIRT2129517	hsa-miR-3529	CLIP-seq
MIRT1432084	hsa-miR-3679-3p	CLIP-seq
MIRT2129518	hsa-miR-3692	CLIP-seq
MIRT2129519	hsa-miR-369-3p	CLIP-seq
MIRT2129520	hsa-miR-379	CLIP-seq
MIRT2129521	hsa-miR-4286	CLIP-seq
MIRT2129522	hsa-miR-429	CLIP-seq
MIRT2129523	hsa-miR-4451	CLIP-seq
MIRT2129524	hsa-miR-4650-3p	CLIP-seq
MIRT1432092	hsa-miR-4704-5p	CLIP-seq
MIRT1432095	hsa-miR-4760-3p	CLIP-seq
MIRT1432107	hsa-miR-664	CLIP-seq
MIRT1432062	hsa-miR-101	CLIP-seq
MIRT1432064	hsa-miR-1283	CLIP-seq
MIRT1432066	hsa-miR-1324	CLIP-seq
MIRT1432067	hsa-miR-144	CLIP-seq
MIRT1432068	hsa-miR-148a	CLIP-seq
MIRT1432069	hsa-miR-148b	CLIP-seq
MIRT1432070	hsa-miR-152	CLIP-seq
MIRT1432071	hsa-miR-2054	CLIP-seq
MIRT1432072	hsa-miR-221	CLIP-seq
MIRT1432073	hsa-miR-222	CLIP-seq
MIRT2129518	hsa-miR-3692	CLIP-seq
MIRT2351098	hsa-miR-4330	CLIP-seq
MIRT2351099	hsa-miR-4506	CLIP-seq
MIRT1432092	hsa-miR-4704-5p	CLIP-seq
MIRT2351100	hsa-miR-4775	CLIP-seq
MIRT1432102	hsa-miR-548v	CLIP-seq
MIRT1432062	hsa-miR-101	CLIP-seq
MIRT1432067	hsa-miR-144	CLIP-seq
MIRT1432062	hsa-miR-101	CLIP-seq
MIRT1432064	hsa-miR-1283	CLIP-seq
MIRT1432067	hsa-miR-144	CLIP-seq
MIRT1432068	hsa-miR-148a	CLIP-seq
MIRT1432069	hsa-miR-148b	CLIP-seq
MIRT1432070	hsa-miR-152	CLIP-seq
MIRT1432072	hsa-miR-221	CLIP-seq
MIRT1432073	hsa-miR-222	CLIP-seq
MIRT1432094	hsa-miR-4719	CLIP-seq
MIRT1432102	hsa-miR-548v	CLIP-seq
MIRT1432105	hsa-miR-587	CLIP-seq
MIRT1432071	hsa-miR-2054	CLIP-seq
MIRT1432105	hsa-miR-587	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0005384	Function	Manganese ion transmembrane transporter activity	IBA
GO:0005765	Component	Lysosomal membrane	IDA	23575229
GO:0005794	Component	Golgi apparatus	IBA
GO:0005794	Component	Golgi apparatus	IDA	22683087
GO:0005794	Component	Golgi apparatus	IEA
GO:0006487	Process	Protein N-linked glycosylation	IMP	22683087
GO:0006816	Process	Calcium ion transport	IDA	32047108
GO:0006816	Process	Calcium ion transport	IEA
GO:0006828	Process	Manganese ion transport	IDA	32047108
GO:0006828	Process	Manganese ion transport	IEA
GO:0006874	Process	Intracellular calcium ion homeostasis	IGI	23569283
GO:0010008	Component	Endosome membrane	IDA	23575229
GO:0015085	Function	Calcium ion transmembrane transporter activity	IBA
GO:0015297	Function	Antiporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0032468	Process	Golgi calcium ion homeostasis	IBA
GO:0032472	Process	Golgi calcium ion transport	IBA
GO:0032472	Process	Golgi calcium ion transport	IDA	23569283
GO:0032588	Component	Trans-Golgi network membrane	IDA	23575229
GO:0033106	Component	Cis-Golgi network membrane	IEA
GO:0033106	Component	Cis-Golgi network membrane	ISS
GO:0035751	Process	Regulation of lysosomal lumen pH	IMP	23569283
GO:0046873	Function	Metal ion transmembrane transporter activity	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IBA
GO:0071421	Process	Manganese ion transmembrane transport	IBA

Other IDs

• MIM: 614726
• HGNC: 30760
• e!Ensembl: ENSG00000134851

Protein

• UniProt ID: Q9HC07
• Protein name: Putative divalent cation/proton antiporter TMEM165 (Transmembrane protein 165) (Transmembrane protein PT27) (Transmembrane protein TPARL)
• Protein function: Putative divalent cation:proton antiporter that exchanges calcium or manganese ions for protons across the Golgi membrane. Mediates the reversible transport of calcium or manganese to the Golgi lumen driven by the proton gradient and possibly th
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01169	UPF0016	98 → 171	Uncharacterized protein family UPF0016	Family
  PF01169	UPF0016	238 → 312	Uncharacterized protein family UPF0016	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:22683087}.
• Sequence:

  MAAAAPGNGRASAPRLLLLFLVPLLWAPAAVRAGPDEDLSHRNKEPPAPAQQLQPQPVAV
  QGPEPARVEKIFTPAAPVHTNKEDPATQTNLGFIHAFVAAISVIIVSELGDKTFFIAAIM
  AMRYNRLTVLAGAMLALGLMTCLSVLFGYATTVIPRVYTYYVSTVLFAIFGIRMLREGLK
  MSPDEGQEELEEVQAELKKKDEEFQRTKLLNGPGDVETGTSITVPQKKWLHFISPIFVQA
  LTLTFLAEWGDRSQLTTIVLAAREDPYGVAVGGTVGHCLCTGLAVIGGRMIAQKISVRTV
  TIIGGIVFLAFAFSALFISPDSGF

• Sequence length: 324

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
TMEM165-congenital disorder of glycosylation	Pathogenic	rs2545501546, rs793888506, rs387907221, rs886037631	RCV003532482 RCV000029179 RCV000029180 RCV000029182	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Aganglionic megacolon	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARBOHYDRATE DEFICIENT GLYCOPROTEIN SYNDROME TYPE 2K	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation	Benign; Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIK	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDERS OF GLYCOSYLATION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioma susceptibility 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HIRSCHSPRUNG DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER CIRRHOSIS, EXPERIMENTAL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TMEM165-related disorder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acoustic Neuroma	Acoustic Neuroma	BEFREE	29392722		★☆☆☆☆ Found in Text Mining only
Acquired Kyphoscoliosis	Acquired Kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Amelogenesis Imperfecta	Amelogenesis imperfecta	GENOMICS_ENGLAND_DG	22683087		★☆☆☆☆ Found in Text Mining only
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	30696097	Associate	★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar disorder	Pubtator	18228528	Associate	★☆☆☆☆ Found in Text Mining only
Bone Diseases, Developmental	Bone Disease	BEFREE	25609749		★☆☆☆☆ Found in Text Mining only
Camurati-Engelmann Syndrome	Diaphyseal dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carbohydrate deficient glycoprotein syndrome type 2k	Congenital disorder of glycosylation	ORPHANET_DG	22683087		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carbohydrate deficient glycoprotein syndrome type 2k	Congenital disorder of glycosylation	GENOMICS_ENGLAND_DG	22683087, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carbohydrate deficient glycoprotein syndrome type 2k	Congenital disorder of glycosylation	UNIPROT_DG	22683087, 23430531, 23575229		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carbohydrate deficient glycoprotein syndrome type 2k	Congenital disorder of glycosylation	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carbohydrate deficient glycoprotein syndrome type 2k	Congenital disorder of glycosylation	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	30015898	Stimulate	★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type II	Congenital disorder of glycosylation	Pubtator	22683087, 30307768	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	22683087, 24720419, 25609749, 27008884, 27401145, 28088503, 28114750, 28270545, 28323990, 29632074, 29702557, 30015898, 30307768, 31415112		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	22683087, 27008884, 28323990, 30015898, 31415112	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital kyphoscoliosis	Congenital kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diaphyseal dysplasia	Diaphyseal dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Endocrine System Diseases	Endocrine system disease	Pubtator	28323990	Associate	★☆☆☆☆ Found in Text Mining only
Epiphyseal dysplasia	Epiphyseal dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	30015898		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30015898		★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic syndrome	Pubtator	30015898	Associate	★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pyle metaphyseal dysplasia	Pyle Metaphyseal Dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
TMEM165-CDG	Congenital Disorder Of Glycosylation	Orphanet			★☆☆☆☆ Found in Text Mining only