TMEM63C

gene
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Also known as DKFZp434P0111CSC1hsCSC1

Summary

TMEM63C (transmembrane protein 63C, HGNC:23787) is a protein-coding gene on chromosome 14q24.3, encoding Osmosensitive cation channel TMEM63C (Q9P1W3). Acts as an osmosensitive cation channel preferentially activated upon hypotonic stress.

Enables calcium-activated cation channel activity. Involved in monoatomic cation transport. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in plasma membrane. Implicated in hereditary spastic paraplegia 87. Biomarker of focal segmental glomerulosclerosis.

Source: NCBI Gene 57156 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): spastic paraplegia 87, autosomal recessive (Strong, GenCC)
  • GWAS associations: 4
  • Clinical variants (ClinVar): 118 total — 4 pathogenic
  • Phenotypes (HPO): 18
  • MANE Select transcript: NM_020431

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23787
Approved symbolTMEM63C
Nametransmembrane protein 63C
Location14q24.3
Locus typegene with protein product
StatusApproved
AliasesDKFZp434P0111, CSC1, hsCSC1
Ensembl geneENSG00000165548
Ensembl biotypeprotein_coding
OMIM619953
Entrez57156

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 retained_intron

ENST00000298351, ENST00000554346, ENST00000554766, ENST00000555338, ENST00000555588, ENST00000556514, ENST00000557408, ENST00000557504, ENST00000890513, ENST00000890514, ENST00000890515, ENST00000890516, ENST00000890517, ENST00000957931

RefSeq mRNA: 1 — MANE Select: NM_020431 NM_020431

CCDS: CCDS45141

Canonical transcript exons

ENST00000298351 — 24 exons

ExonStartEnd
ENSE000010940047723869477238767
ENSE000010940107724929177249458
ENSE000010940157724660977246674
ENSE000010940187724876777248872
ENSE000010940197722542477225461
ENSE000010940247724594077246026
ENSE000010940257724434977244455
ENSE000010940267724234777242469
ENSE000010940277723960377239726
ENSE000010940287723662477236732
ENSE000010940297724047577240608
ENSE000010940307724834777248509
ENSE000010940347724290377243056
ENSE000010940357723941277239492
ENSE000010940377723345277233500
ENSE000010940397725178977251898
ENSE000011586807725652677259495
ENSE000014217027721344677213508
ENSE000025254047718179877181894
ENSE000036121037722000677220087
ENSE000036384147725330577253376
ENSE000036455627721949877219577
ENSE000037850847721880177218963
ENSE000037907887723158877231730

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 94.14.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7467 / max 294.7520, expressed in 454 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1407670.7671312
1407680.2339119
1407660.2095113
1407690.133573
1407610.12905
1407620.07854
1407580.07606
1407590.06086
1407600.04734
1407640.01113

Top tissues by expression

248 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212994.14gold quality
cerebellar hemisphereUBERON:000224594.11gold quality
right hemisphere of cerebellumUBERON:001489093.96gold quality
cerebellumUBERON:000203793.69gold quality
cerebellar vermisUBERON:000472092.00gold quality
pituitary glandUBERON:000000791.46gold quality
adenohypophysisUBERON:000219691.23gold quality
islet of LangerhansUBERON:000000688.36gold quality
dorsal root ganglionUBERON:000004486.18gold quality
lateral nuclear group of thalamusUBERON:000273685.01gold quality
pancreatic ductal cellCL:000207984.56silver quality
hypothalamusUBERON:000189884.52gold quality
cortical plateUBERON:000534384.24gold quality
right frontal lobeUBERON:000281084.18gold quality
prefrontal cortexUBERON:000045183.91gold quality
substantia nigra pars compactaUBERON:000196583.80gold quality
frontal cortexUBERON:000187083.02gold quality
substantia nigra pars reticulataUBERON:000196682.33silver quality
lateral globus pallidusUBERON:000247682.13silver quality
superior vestibular nucleusUBERON:000722782.00gold quality
neocortexUBERON:000195081.96gold quality
brainUBERON:000095581.79gold quality
Brodmann (1909) area 9UBERON:001354081.60gold quality
ventral tegmental areaUBERON:000269181.41silver quality
dorsolateral prefrontal cortexUBERON:000983480.83gold quality
nucleus accumbensUBERON:000188280.77gold quality
dorsal plus ventral thalamusUBERON:000189780.41silver quality
forebrainUBERON:000189080.38gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.35gold quality
endothelial cellCL:000011580.08gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.35
E-CURD-10no0.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

112 targeting TMEM63C, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-4283100.0066.422097
HSA-MIR-4481100.0066.421669
HSA-MIR-807599.9767.20962
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-185-3P99.9567.011743
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-990299.8969.152250
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-449299.8768.253611
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-149-3P99.7268.223963
HSA-MIR-1296-3P99.7264.04636
HSA-MIR-117999.7168.701040
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-7157-5P99.6669.331829
HSA-MIR-10394-5P99.6566.831852

Literature-anchored findings (GeneRIF, showing 3)

  • Tmem63c is a potential pro-survival factor in angiotensin II-treated human podocytes. (PMID:32750436)
  • TMEM63C, a Potential Novel Target for Albuminuria Development, Is Regulated by MicroRNA-564 and Transforming Growth Factor beta in Human Renal Cells. (PMID:33080601)
  • TMEM63C mutations cause mitochondrial morphology defects and underlie hereditary spastic paraplegia. (PMID:35718349)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotmem63cENSDARG00000004158
mus_musculusTmem63cENSMUSG00000034145
rattus_norvegicusTmem63cENSRNOG00000011334

Paralogs (2): TMEM63B (ENSG00000137216), TMEM63A (ENSG00000196187)

Protein

Protein identifiers

Osmosensitive cation channel TMEM63CQ9P1W3 (reviewed: Q9P1W3)

Alternative names: Calcium permeable stress-gated cation channel 1, Transmembrane protein 63C

All UniProt accessions (6): Q9P1W3, G3V2V1, G3V3H0, G3V3S4, G3V3S9, G3V4J5

UniProt curated annotations — full annotation on UniProt →

Function. Acts as an osmosensitive cation channel preferentially activated upon hypotonic stress. In contrast to TMEM63B, does not show phospholipid scramblase activity. Enriched in mitochondria-ER contact sites where it may regulate the metabolite flux and organelles’ morphologies in response to osmotic changes. In particular may regulate mitochondrial motility and function in motor neuron axons. Required for the functional integrity of the kidney glomerular filtration barrier.

Subunit / interactions. Monomer.

Subcellular location. Endoplasmic reticulum membrane. Cell membrane.

Tissue specificity. Expressed in podocytes of kidney glomeruli. Significantly reduced expression in patients with focal segmental glomerulosclerosis.

Disease relevance. Spastic paraplegia 87, autosomal recessive (SPG87) [MIM:619966] A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPG87 is characterized by onset of lower limb spasticity in infancy or early childhood, and lack of upper limbs and bulbar regions involvement. Affected individuals have mildly delayed walking, spastic gait, and hyperreflexia. Some patients may also have mild intellectual disability or speech problems. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Activated by hyperosmotic shock after mannitol treatment.

Similarity. Belongs to the CSC1 (TC 1.A.17) family.

RefSeq proteins (1): NP_065164* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003864CSC1/OSCA1-like_7TMDomain
IPR027815CSC1/OSCA1-like_cytDomain
IPR032880CSC1/OSCA1-like_NDomain
IPR045122Csc1-likeFamily

Pfam: PF02714, PF13967, PF14703

Catalyzed reactions (Rhea), 1 shown:

  • Ca(2+)(in) = Ca(2+)(out) (RHEA:29671)

UniProt features (31 total): topological domain 12, transmembrane region 11, modified residue 2, sequence variant 2, sequence conflict 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P1W3-F174.760.31

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 77, 80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GOCC_VACUOLAR_MEMBRANE, GOBP_MONOATOMIC_CATION_TRANSPORT, GTGCCTT_MIR506, chr14q24, GOBP_RENAL_FILTRATION, GOBP_TRANSMEMBRANE_TRANSPORT, GOBP_RENAL_SYSTEM_PROCESS, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_LIPID_TRANSPORTER_ACTIVITY, GOMF_GATED_CHANNEL_ACTIVITY, GOMF_PASSIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_MONOATOMIC_CATION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_TRANSMEMBRANE_SIGNALING_RECEPTOR_ACTIVITY

GO Biological Process (5): glomerular filtration (GO:0003094), monoatomic cation transport (GO:0006812), monoatomic ion transport (GO:0006811), monoatomic ion transmembrane transport (GO:0034220), monoatomic cation transmembrane transport (GO:0098655)

GO Molecular Function (2): calcium-activated cation channel activity (GO:0005227), osmolarity-sensing monoatomic cation channel activity (GO:1990760)

GO Cellular Component (5): lysosomal membrane (GO:0005765), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
monoatomic ion transport2
renal filtration1
transport1
transmembrane transport1
monoatomic cation transport1
monoatomic ion transmembrane transport1
monoatomic ion-gated channel activity1
ligand-gated monoatomic cation channel activity1
osmosensor activity1
monoatomic cation channel activity1
gated channel activity1
lysosome1
lytic vacuole membrane1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

446 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMEM63CINCENPQ9NQS7955
TMEM63CKCNJ6P48051844
TMEM63CAURKBQ96GD4796
TMEM63CSTRIP1Q5VSL9547
TMEM63COTULINLQ9NUU6521
TMEM63CEFSO43281520
TMEM63CCCDC106Q9BWC9495
TMEM63CSTRNO43815480
TMEM63CSNX15Q9NRS6463
TMEM63CVWA5AO00534459
TMEM63CRNF150Q9ULK6457
TMEM63CTMEM234Q8WY98453
TMEM63CPPP2R1AP30153444
TMEM63CTMEM120AQ9BXJ8444
TMEM63CCDCA8Q53HL2434
TMEM63CRNPC3Q96LT9434

IntAct

3 interactions, top by confidence:

ABTypeScore
NPPAA2ML1psi-mi:“MI:0914”(association)0.530
TMEM63CGPR89Apsi-mi:“MI:0914”(association)0.350

BioGRID (41): TMEM63C (Affinity Capture-RNA), TMEM63C (Proximity Label-MS), TMEM199 (Affinity Capture-MS), DNAJC18 (Affinity Capture-MS), RNFT1 (Affinity Capture-MS), PIGH (Affinity Capture-MS), OSBP (Affinity Capture-MS), RAB10 (Affinity Capture-MS), FAM63A (Affinity Capture-MS), TMEM63A (Affinity Capture-MS), TMEM63B (Affinity Capture-MS), PLD1 (Affinity Capture-MS), GPR89A (Affinity Capture-MS), SLC30A6 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS)

ESM2 similar proteins: A0A452G813, A0A8V0ZB02, A1L3G9, A2AWR3, A9LIW2, B6HTR9, D3ZNF5, F4I248, F4JCY2, O35379, O57428, O94886, O94911, P08983, Q059Y8, Q06538, Q09427, Q09428, Q09429, Q17JQ7, Q3KTM2, Q3TWI9, Q4R7U0, Q4V8U5, Q5GH22, Q5GH60, Q5GH68, Q5R826, Q5R9A7, Q5T3F8, Q5YCC5, Q6NP91, Q6PP77, Q6UR05, Q7Q5R7, Q7Z3F1, Q7Z402, Q8C428, Q8CBX0, Q8CG09

Diamond homologs: A0A452G813, A0A8V0ZB02, D3ZNF5, O94886, Q3TWI9, Q5R826, Q5T3F8, Q6NP91, Q8CBX0, Q91YT8, Q9P1W3, X1WEM4, Q9SZT4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

118 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic4
Likely pathogenic0
Uncertain significance92
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1698436NM_020431.4(TMEM63C):c.1641_1656delinsGGC (p.Asn547fs)Pathogenic
1698437NM_020431.4(TMEM63C):c.1216del (p.Trp406fs)Pathogenic
1698438NM_020431.4(TMEM63C):c.585C>G (p.Tyr195Ter)Pathogenic
1698439NM_020431.4(TMEM63C):c.1572dup (p.Tyr525fs)Pathogenic

SpliceAI

6003 predictions. Top by Δscore:

VariantEffectΔscore
14:77141598:CTCA:Cdonor_loss1.0000
14:77141599:TCA:Tdonor_loss1.0000
14:77141600:CAC:Cdonor_loss1.0000
14:77141601:A:ACdonor_gain1.0000
14:77141602:C:CCdonor_gain1.0000
14:77141602:C:CTdonor_loss1.0000
14:77141602:CCGAG:Cdonor_gain1.0000
14:77219978:A:AGacceptor_gain1.0000
14:77219979:C:Gacceptor_gain1.0000
14:77219985:T:TAacceptor_gain1.0000
14:77219996:T:Aacceptor_gain1.0000
14:77219997:G:Aacceptor_gain1.0000
14:77220000:T:Aacceptor_gain1.0000
14:77220002:GCA:Gacceptor_loss1.0000
14:77220002:GCAGC:Gacceptor_loss1.0000
14:77220003:CAGCC:Cacceptor_loss1.0000
14:77220004:A:ACacceptor_loss1.0000
14:77220004:A:AGacceptor_gain1.0000
14:77220004:AGCCT:Aacceptor_gain1.0000
14:77220005:G:GTacceptor_gain1.0000
14:77220005:GC:Gacceptor_gain1.0000
14:77220005:GCC:Gacceptor_gain1.0000
14:77220005:GCCT:Gacceptor_gain1.0000
14:77220005:GCCTG:Gacceptor_gain1.0000
14:77220085:AAGG:Adonor_loss1.0000
14:77220085:AAGGT:Adonor_loss1.0000
14:77220086:AGG:Adonor_loss1.0000
14:77220086:AGGTG:Adonor_loss1.0000
14:77220087:GGT:Gdonor_loss1.0000
14:77220087:GGTG:Gdonor_loss1.0000

AlphaMissense

5363 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:77240578:T:AV345D0.999
14:77248842:A:CS614R0.999
14:77248844:C:AS614R0.999
14:77248844:C:GS614R0.999
14:77249327:G:CR636P0.999
14:77239603:G:CR269S0.998
14:77239603:G:TR269S0.998
14:77239623:G:CR276P0.998
14:77242429:T:AW383R0.998
14:77242429:T:CW383R0.998
14:77242468:T:AW396R0.998
14:77242468:T:CW396R0.998
14:77242903:G:CW396C0.998
14:77242903:G:TW396C0.998
14:77240515:T:CL324P0.997
14:77248355:T:GF537C0.997
14:77248872:G:AG624R0.997
14:77248872:G:CG624R0.997
14:77248872:G:TG624W0.997
14:77249291:G:AG624E0.997
14:77233467:T:GF170C0.996
14:77238707:T:CL222P0.996
14:77239454:C:GC256W0.996
14:77239471:T:CL262P0.996
14:77239492:G:CR269T0.996
14:77240575:T:CF344S0.996
14:77248354:T:CF537L0.996
14:77248356:C:AF537L0.996
14:77248356:C:GF537L0.996
14:77248824:A:CS608R0.996

dbSNP variants (sampled 300 via entrez): RS1000007630 (14:77227635 C>T), RS1000062954 (14:77181258 G>T), RS1000075375 (14:77186749 G>C), RS1000185666 (14:77210515 A>G), RS1000188495 (14:77215763 A>C,G), RS1000199368 (14:77259927 T>C), RS1000239985 (14:77222024 G>A), RS1000249727 (14:77255362 G>A,C), RS1000281501 (14:77181460 G>A,T), RS1000389790 (14:77216357 A>C,T), RS1000407496 (14:77216036 C>T), RS1000442512 (14:77257634 C>T), RS1000494513 (14:77203259 G>A), RS1000538982 (14:77250515 C>T), RS1000539527 (14:77198602 A>G)

Disease associations

OMIM: gene MIM:619953 | disease phenotypes: MIM:619966

GenCC curated gene-disease

DiseaseClassificationInheritance
spastic paraplegia 87, autosomal recessiveStrongAutosomal recessive

Mondo (1): spastic paraplegia 87, autosomal recessive (MONDO:0031019)

Orphanet (1): Autosomal recessive spastic paraplegia type 87 (Orphanet:631088)

HPO phenotypes

18 total (18 of 18 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000486Strabismus
HP:0000639Nystagmus
HP:0000750Delayed speech and language development
HP:0001256Mild intellectual disability
HP:0001260Dysarthria
HP:0001332Dystonia
HP:0001347Hyperreflexia
HP:0002061Lower limb spasticity
HP:0002064Spastic gait
HP:0002194Delayed gross motor development
HP:0002395Lower limb hyperreflexia
HP:0002938Lumbar hyperlordosis
HP:0003487Babinski sign
HP:0003593Infantile onset
HP:0006986Upper limb spasticity
HP:0007350Upper limb hyperreflexia
HP:0011463Childhood onset

GWAS associations

4 associations (top):

StudyTraitp-value
GCST003434_12Obsessive-compulsive symptoms9.000000e-06
GCST004070_19Cerebrospinal P-tau181p levels4.000000e-06
GCST008155_70Waist-hip ratio1.000000e-06
GCST010572_6Sweet taste preference2.000000e-06

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007802obsessive-compulsive symptom measurement
EFO:0004763p-tau measurement
EFO:0004343waist-hip ratio
EFO:0010156sweet liking measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression, increases methylation4
Benzo(a)pyreneaffects methylation, decreases methylation, increases methylation2
Cadmium Chloridedecreases expression2
aminomethylphosphonic acid (AMPA)decreases expression1
propionaldehydeincreases expression1
bisphenol Adecreases methylation1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
aflatoxin B2increases methylation1
pentanalincreases expression1
abrinedecreases expression1
Sunitinibincreases expression1
Aldehydesincreases expression1
Arsenicaffects methylation1
Estradiolincreases expression1
Niclosamideincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Triclosanincreases expression1
2,4-Dichlorophenoxyacetic Aciddecreases expression1
Aflatoxin B1decreases methylation1
Okadaic Acidincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_YA84IDG-HEK293T-TMEM63C-V5-OETransformed cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.