CAPS

Summary

CAPS (calcyphosine, HGNC:1487) is a protein-coding gene on chromosome 19p13.3, encoding Calcyphosin (Q13938). Calcium-binding protein.

This gene encodes a calcium-binding protein, which may play a role in the regulation of ion transport. A similar protein was first described as a potentially important regulatory protein in the dog thyroid and was termed as R2D5 antigen in rabbit. Alternative splicing of this gene generates two transcript variants.

Source: NCBI Gene 828 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 66 total
• MANE Select transcript: NM_004058

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1487
Approved symbol	CAPS
Name	calcyphosine
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	CAPS1, MGC126562
Ensembl gene	ENSG00000105519
Ensembl biotype	protein_coding
OMIM	114212
Entrez	828

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 retained_intron

ENST00000452990, ENST00000585541, ENST00000588776, ENST00000588865, ENST00000590428, ENST00000852353, ENST00000852354, ENST00000852355, ENST00000852356, ENST00000852357, ENST00000852358, ENST00000961097

RefSeq mRNA: 2 — MANE Select: NM_004058 NM_004058, NM_080590

CCDS: CCDS12156, CCDS45934

Canonical transcript exons

ENST00000588776 — 5 exons

Exon	Start	End
ENSE00000666175	5914940	5915146
ENSE00002930628	5914254	5914309
ENSE00003796938	5914563	5914740
ENSE00003844488	5914385	5914489
ENSE00003894180	5915221	5916211

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 99.94.

FANTOM5 (CAGE): breadth broad, TPM avg 6.7864 / max 591.2492, expressed in 605 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173439	6.6301	597
173438	0.1270	58
173440	0.0292	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.94	gold quality
bronchus	UBERON:0002185	99.88	gold quality
right uterine tube	UBERON:0001302	99.82	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	99.54	gold quality
nasal cavity epithelium	UBERON:0005384	98.89	gold quality
mucosa of paranasal sinus	UBERON:0005030	98.54	gold quality
trachea	UBERON:0003126	98.38	gold quality
pancreatic ductal cell	CL:0002079	97.80	silver quality
oviduct epithelium	UBERON:0004804	96.69	gold quality
nasal cavity mucosa	UBERON:0001826	96.58	gold quality
fallopian tube	UBERON:0003889	96.53	gold quality
superior vestibular nucleus	UBERON:0007227	95.60	gold quality
tibial nerve	UBERON:0001323	94.92	gold quality
epithelium of nasopharynx	UBERON:0001951	94.68	gold quality
vena cava	UBERON:0004087	94.25	gold quality
kidney epithelium	UBERON:0004819	94.16	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	94.02	gold quality
spinal cord	UBERON:0002240	93.93	gold quality
tendon of biceps brachii	UBERON:0008188	93.06	gold quality
medulla oblongata	UBERON:0001896	93.00	gold quality
seminal vesicle	UBERON:0000998	92.81	gold quality
left ventricle myocardium	UBERON:0006566	92.60	gold quality
left uterine tube	UBERON:0001303	92.33	gold quality
body of stomach	UBERON:0001161	92.21	gold quality
fundus of stomach	UBERON:0001160	92.07	gold quality
ventral tegmental area	UBERON:0002691	91.76	gold quality
right lung	UBERON:0002167	91.66	gold quality
cardia of stomach	UBERON:0001162	91.55	gold quality
parotid gland	UBERON:0001831	91.35	silver quality
caput epididymis	UBERON:0004358	91.21	gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 15.

Experiment	Marker?	Max mean expression
E-HCAD-15	yes	7159.99
E-MTAB-10283	yes	6028.90
E-MTAB-10287	yes	5399.68
E-CURD-126	yes	5160.71
E-CURD-114	yes	4874.52
E-MTAB-6653	yes	4392.74
E-HCAD-1	yes	4282.69
E-MTAB-8221	yes	4272.67
E-MTAB-6701	yes	3358.78
E-CURD-122	yes	2752.58
E-MTAB-6308	yes	2347.85
E-HCAD-38	yes	1894.99
E-GEOD-130148	yes	1780.88
E-HCAD-10	yes	19.66
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

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

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-210-5P	98.57	64.37	832
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-6765-3P	97.83	64.59	1165
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-3663-5P	97.01	64.84	713
HSA-MIR-4485-5P	95.91	59.69	198
HSA-MIR-4471	95.11	66.84	755
HSA-MIR-8059	95.11	66.30	646

Literature-anchored findings (GeneRIF, showing 5)

• Results demonstrated the ubiquitous overexpressions of E-FABP and CAPS in EC and the correlations to the clinicopathologic parameters. CAPS might be a potential prognostic factor for survival in patients with EC (PMID:18729184)
• These results describe the crystal structure of Ca(2+)-loaded calcyphosine up to 2.65 A resolution and reveal a protein containing two pairs of Ca(2+)-binding EF-hand motifs. (PMID:18775726)
• The calcyphosine crystal diffracted to 2.8 A and belonged to space group P2(1)2(1)2, with the unit cell parameters a=70.39 A, b=132.02 A, c=46.20 A. (PMID:19275752)
• The results indicated that the autosomal recessive homozygous mutation, p.Leu127Trpfs, in CAPS might be a maternal effect causative mutation of RPL pathogenesis. (PMID:30339840)
• Calcyphosine promotes the proliferation of glioma cells and serves as a potential therapeutic target. (PMID:34370292)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	TpnC47D	FBGN0010423
drosophila_melanogaster	TpnC73F	FBGN0010424
drosophila_melanogaster	TpnC41C	FBGN0013348

Paralogs (5): PHF24 (ENSG00000122733), CAPSL (ENSG00000152611), CAPS2 (ENSG00000180881), EFCAB6 (ENSG00000186976), SPATA21 (ENSG00000187144)

Protein

Protein identifiers

Calcyphosin — Q13938 (reviewed: Q13938)

Alternative names: Calcyphosine

All UniProt accessions (4): Q13938, A0A384NYV7, A0A499FJ41, K7ES72

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-binding protein. May play a role in cellular signaling events (Potential).

Subunit / interactions. Monomer. Does not form oligomers in the presence of calcium.

Subcellular location. Cytoplasm.

Isoforms (3)

UniProt ID	Names	Canonical?
Q13938-1	1	yes
Q13938-3	2
Q13938-4	3

RefSeq proteins (2): NP_004049, NP_542157 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR051581	Ca-bind	Family

Pfam: PF13499

UniProt features (41 total): binding site 14, helix 11, domain 4, strand 3, splice variant 2, sequence variant 2, turn 2, chain 1, modified residue 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3E3R	X-RAY DIFFRACTION	2.65

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13938-F1	69.49	0.04

Functional residue map

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

Ligand- & substrate-binding residues (14): 131; 156; 158; 160; 162; 167; 192; 194; 196; 203; 120; 122 …

Post-translational modifications (1): 126

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 73 (showing top): CHANDRAN_METASTASIS_DN, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, WTGAAAT_UNKNOWN, AACTTT_UNKNOWN, CREBP1_01, chr19p13, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, WHITFIELD_CELL_CYCLE_S, BCAT_BILD_ET_AL_UP, MYC_UP.V1_UP, SRC_UP.V1_UP, GLI1_TARGET_GENES, HES2_TARGET_GENES, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2

GO Biological Process (1): intracellular signal transduction (GO:0035556)

GO Molecular Function (2): calcium ion binding (GO:0005509), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleoplasm (GO:0005654), cytosol (GO:0005829), plasma membrane (GO:0005886), vesicle (GO:0031982), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
intracellular anatomical structure	2
signal transduction	1
metal ion binding	1
cation binding	1
nuclear lumen	1
cytoplasm	1
membrane	1
cell periphery	1
membrane-bounded organelle	1

Protein interactions and networks

STRING

945 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CAPS	Q32Q12	Q32Q12	481
CAPS	CAPG	P40121	423
CAPS	SYT1	P21579	422
CAPS	X6REF7	X6REF7	415
CAPS	CAPS2	Q9BXY5	355
CAPS	SERPINB1	P30740	344
CAPS	CATSPERD	Q86XM0	344
CAPS	CFAP53	Q96M91	333
CAPS	ANXA3	P12429	304
CAPS	CALML4	Q96GE6	295
CAPS	RPLP2	P05387	294
CAPS	CIB1	Q99828	287
CAPS	CIMAP3	Q8TCI5	276
CAPS	TPPP3	Q9BW30	271
CAPS	MNS1	Q8NEH6	269

IntAct

13 interactions, top by confidence:

A	B	Type	Score
TUBB2B	EML2	psi-mi:“MI:0914”(association)	0.530
FOXJ1	PEX14	psi-mi:“MI:0914”(association)	0.530
HTRA4	PSMD12	psi-mi:“MI:0914”(association)	0.350
CAPS	TUBAL3	psi-mi:“MI:0914”(association)	0.350
ZC2HC1B	TUBB4A	psi-mi:“MI:0914”(association)	0.350
TBC1D28	CAPS	psi-mi:“MI:0914”(association)	0.350
TUBB2B	POTEF	psi-mi:“MI:0914”(association)	0.350
IGSF8	SCAMP3	psi-mi:“MI:0914”(association)	0.350
RAB6C	CAPS	psi-mi:“MI:0914”(association)	0.350
CDH1	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (28): CAPS (Affinity Capture-MS), CAPS (Proximity Label-MS), CAPS (Affinity Capture-MS), CAPS (Affinity Capture-MS), CAPS (Affinity Capture-MS), CAPS (Affinity Capture-RNA), TUBB2A (Affinity Capture-MS), TUBB (Affinity Capture-MS), CAPS (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), TUBAL3 (Affinity Capture-MS), TUBA4A (Affinity Capture-MS), CAPS (Affinity Capture-MS), CAPS (Affinity Capture-MS), TUBB3 (Affinity Capture-MS)

ESM2 similar proteins: A0JPF9, A2A6C4, A4FUG7, A5PK74, A6H751, F7E727, O43304, O95382, O95398, P0C025, P35523, P48760, P50168, P51657, P54265, P54777, Q05932, Q08CY5, Q09013, Q13938, Q15477, Q16549, Q1L5Z9, Q3U5Q7, Q4KLY6, Q5MFW3, Q5RER0, Q62849, Q63ZY6, Q643R3, Q6NVG1, Q75NR7, Q76MJ5, Q7Z5J1, Q8CJI3, Q8IUH8, Q8N6F8, Q8NFF5, Q8R2S1, Q8WWF5

Diamond homologs: P10463, P41150, P80363, P80364, Q0VCC0, Q13938, Q6P8Y1, Q8WWF8, Q9GKR6, P82978, Q03975, Q3E9C0, Q66L49, Q8BUG5, Q9FMP5, Q9S9V0, Q9BXY5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	6
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1239 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:5914982:T:C	F188L	0.994
19:5914984:T:A	F188L	0.994
19:5914984:T:G	F188L	0.994
19:5915236:T:C	F248L	0.988
19:5915238:C:A	F248L	0.988
19:5915238:C:G	F248L	0.988
19:5915287:T:C	F265L	0.988
19:5915289:C:A	F265L	0.988
19:5915289:C:G	F265L	0.988
19:5915237:T:C	F248S	0.985
19:5915260:A:C	S256R	0.979
19:5915262:T:A	S256R	0.979
19:5915262:T:G	S256R	0.979
19:5915311:T:A	W273R	0.979
19:5915311:T:C	W273R	0.979
19:5915120:T:C	F234L	0.970
19:5915122:C:A	F234L	0.970
19:5915122:C:G	F234L	0.970
19:5914723:T:C	F168L	0.967
19:5914725:C:A	F168L	0.967
19:5914725:C:G	F168L	0.967
19:5915108:T:C	F230L	0.964
19:5915110:C:A	F230L	0.964
19:5915110:C:G	F230L	0.964
19:5915237:T:G	F248C	0.962
19:5914983:T:C	F188S	0.961
19:5915016:T:A	V199E	0.954
19:5915288:T:C	F265S	0.954
19:5915313:G:C	W273C	0.952
19:5915313:G:T	W273C	0.952

dbSNP variants (sampled 300 via entrez): RS1000127676 (19:5914032 G>T), RS1001065514 (19:5912459 C>A,T), RS1001380062 (19:5915783 A>G), RS1001704498 (19:5915805 A>G), RS1002892498 (19:5915963 T>G), RS1003189277 (19:5913402 A>C), RS1003386038 (19:5914167 T>A,C), RS1003455023 (19:5915028 A>C,G), RS1003492180 (19:5914569 C>T), RS1004595470 (19:5913769 G>A,C,T), RS1005166857 (19:5915582 G>A,T), RS1005207150 (19:5916170 T>A), RS1005342986 (19:5916418 C>T), RS1007410344 (19:5915551 C>T), RS1007509858 (19:5916610 TCC>T)

Disease associations

OMIM: gene MIM:114212 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	decreases expression, increases abundance, increases expression	3
bisphenol A	decreases methylation, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Estradiol	decreases expression, increases expression	2
Genistein	increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
methylmercuric chloride	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
azoxystrobin	decreases expression	1
deguelin	decreases expression	1
pyrimidifen	decreases expression	1
clothianidin	decreases expression	1
abrine	decreases expression	1
pyrachlostrobin	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Antimycin A	decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Ethinyl Estradiol	increases expression	1
Hydrogen Peroxide	affects expression	1
Niclosamide	increases expression	1
Paraquat	decreases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	decreases expression	1

Clinical trials (associated diseases)

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