TMEM240 (transmembrane protein 240)

Gene

• Entrez ID: 339453
• Gene name: Transmembrane protein 240
• Gene symbol: TMEM240
• Synonyms (NCBI Gene): C1orf70, SCA21
• Chromosome: 1
• Chromosome location: 1p36.33
• Summary: This gene encodes a transmembrane-domain containing protein found in the brain and cerebellum. Mutations in this gene result in spinocerebellar ataxia 21. [provided by RefSeq, Dec 2014]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs606231451	G>A	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs606231452	G>A,C	Pathogenic	Synonymous variant, coding sequence variant, stop gained
rs606231453	G>A	Pathogenic	Coding sequence variant, missense variant
rs606231454	G>A	Pathogenic	Coding sequence variant, missense variant
rs606231455	G>A	Pathogenic	Coding sequence variant, missense variant
rs1045410944	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs1057518011	C>T	Likely-pathogenic	Missense variant, coding sequence variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005886	Component	Plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0045202	Component	Synapse	IEA
GO:0097060	Component	Synaptic membrane	IBA
GO:0097060	Component	Synaptic membrane	IEA
GO:0097060	Component	Synaptic membrane	ISS
GO:0098688	Component	Parallel fiber to Purkinje cell synapse	IEA
GO:0098839	Component	Postsynaptic density membrane	IEA
GO:0150053	Component	Cerebellar climbing fiber to Purkinje cell synapse	IEA
GO:0160045	Component	TMEM240-body	IEA

Other IDs

• MIM: 616101
• HGNC: 25186
• e!Ensembl: ENSG00000205090

Protein

• UniProt ID: Q5SV17
• Protein name: Transmembrane protein 240
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15207	TMEM240	1 → 173	TMEM240 family	Family

• Sequence:

  MSMSANTMIFMILGASVVMAIACLMDMNALLDRFHNYILPHLRGEDRVCHCNCGRHHIHY
  VIPYDGDQSVVDASENYFVTDSVTKQEIDLMLGLLLGFCISWFLVWMDGVLHCAVRAWRA
  GRRYDGSWTWLPKLCSLRELGRRPHRPFEEAAGNMVHVKQKLYHNGHPSPRHL

• Sequence length: 173

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
Spinocerebellar ataxia type 21	Likely pathogenic; Pathogenic	rs2100695149, rs606231451, rs606231452	RCV001647208 RCV000148344 RCV000148345	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Intellectual disability	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 21	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TMEM240-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Akinesia	Akinesia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ataxia, Spinocerebellar	Spinocerebellar Ataxia	BEFREE	26813285		★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	32705938	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	35715741	Inhibit	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	40691650	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar Ataxia	Cerebellar ataxia	Pubtator	26813285, 33851480	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Diseases	Cerebellar diseases	Pubtator	32705938	Associate	★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	32705938	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	23867710, 32398064	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	32705938	Associate	★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysgraphia	Dysgraphia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	25070513		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	25070513		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental Retardation	Mental retardation	BEFREE	25070513		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Parkinsonian Disorders	Parkinson Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Progressive cerebellar ataxia	Cerebellar Ataxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia 11	Spinocerebellar ataxia	Pubtator	26813285	Associate	★☆☆☆☆ Found in Text Mining only
SPINOCEREBELLAR ATAXIA 21	Spinocerebellar Ataxia	GENOMICS_ENGLAND_DG	18418688, 25070513		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 21	Spinocerebellar Ataxia	BEFREE	25070513, 26813285, 30184469, 30522958		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 21	Spinocerebellar Ataxia	ORPHANET_DG	25070513		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 21	Spinocerebellar Ataxia	UNIPROT_DG	25070513, 29053796		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar ataxia 21	Spinocerebellar ataxia	Pubtator	26813285, 33851480	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 21	Spinocerebellar Ataxia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 21	Spinocerebellar Ataxia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar ataxia type 21	Spinocerebellar Ataxia	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Tremor	Tremor	Pubtator	26813285	Associate	★☆☆☆☆ Found in Text Mining only