Gene Gene information from NCBI Gene database.
Entrez ID 54499
Gene name Transmembrane and coiled-coil domains 1
Gene symbol TMCO1
Synonyms (NCBI Gene)
CFSMR1HP10122PCIA3PNAS-136TMCC4
Chromosome 1
Chromosome location 1q24.1
Summary This locus encodes a transmembrane protein. Mutations at this locus have been associated with craniofacial dysmorphism, skeletal anomalies, and cognitive disability. Mutations at this locus have also been associated with open angle glaucoma blindness. Alt
SNPs SNP information provided by dbSNP.
7
SNP ID Visualize variation Clinical significance Consequence
rs201213306 G>A Pathogenic Non coding transcript variant, coding sequence variant, stop gained
rs372701032 C>G,T Pathogenic Intron variant
rs765379963 G>A Pathogenic Stop gained, non coding transcript variant, coding sequence variant
rs765824628 G>A Pathogenic, uncertain-significance Stop gained, non coding transcript variant, coding sequence variant
rs1247427997 G>A,T Pathogenic Synonymous variant, non coding transcript variant, coding sequence variant, stop gained
miRNA miRNA information provided by mirtarbase database.
647
miRTarBase ID miRNA Experiments Reference
MIRT005185 hsa-miR-30a-5p pSILAC 18668040
MIRT005185 hsa-miR-30a-5p Proteomics;Other 18668040
MIRT717025 hsa-miR-2681-3p HITS-CLIP 19536157
MIRT717024 hsa-miR-96-3p HITS-CLIP 19536157
MIRT717023 hsa-miR-1250-3p HITS-CLIP 19536157
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
29
GO ID Ontology Definition Evidence Reference
GO:0000139 Component Golgi membrane IEA
GO:0001503 Process Ossification IEA
GO:0001503 Process Ossification ISS
GO:0005262 Function Calcium channel activity IBA
GO:0005262 Function Calcium channel activity IDA 27212239
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
614123 18188 ENSG00000143183
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9UM00
Protein name Calcium load-activated calcium channel (CLAC channel) (GEL complex subunit TMCO1) (Transmembrane and coiled-coil domain-containing protein 1) (Transmembrane and coiled-coil domains protein 4) (Xenogeneic cross-immune protein PCIA3)
Protein function Endoplasmic reticulum (ER) calcium-selective channel preventing intracellular Ca2(+) stores from overfilling and maintaining calcium homeostasis in the ER (PubMed:27212239). In response to endoplasmic reticulum (ER) Ca2(+) overloading, assembles
PDB 6W6L
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01956 EMC3_TMCO1 49 217 Integral membrane protein EMC3/TMCO1-like Family
Tissue specificity TISSUE SPECIFICITY: Widely expressed in adult and fetal tissues, with higher levels in thymus, prostate, testis and small intestine and lower levels in brain, placenta, lung and kidney (PubMed:10393320, PubMed:20018682). Present in most tissues in the eye
Sequence
Sequence length 239
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
16
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 Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Cerebro-facio-thoracic dysplasia Likely pathogenic; Pathogenic rs765379963 RCV003389727
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1 Likely pathogenic; Pathogenic rs1197771764, rs929157192, rs786204789, rs372701032, rs765824628, rs752176040, rs765379963, rs201213306 RCV001783873
RCV002267201
RCV002293406
RCV000169680
RCV000203247
View all (4 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
TMCO1-related disorder Likely pathogenic; Pathogenic rs752176040 RCV003419799
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
BONE DISEASES, DEVELOPMENTAL CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CEREBROFACIOTHORACIC DYSPLASIA Disgenet, Orphanet
Disgenet, Orphanet
Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL MUSCULOSKELETAL ANOMALIES Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Accessory nipple Accessory Nipple HPO_DG
★☆☆☆☆
Found in Text Mining only
Angle Closure Glaucoma Angle Closure Glaucoma BEFREE 25489222
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect HPO_DG
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Bipolar Disorder Bipolar disorder Pubtator 24387768 Associate
★☆☆☆☆
Found in Text Mining only
Bone Diseases, Developmental Bone Disease CTD_human_DG 20018682
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Brachycephaly Brachycephaly HPO_DG
★☆☆☆☆
Found in Text Mining only
Byzanthine arch palate High palate HPO_DG
★☆☆☆☆
Found in Text Mining only
Cerebral cortical atrophy Cerebral cortical atrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Cerebrofaciothoracic Dysplasia Cerebrofaciothoracic Dysplasia CLINVAR_DG 20018682, 23320496, 24194475, 24424126
★★☆☆☆
Found in Text Mining + Unknown/Other Associations