CABP5

Summary

CABP5 (calcium binding protein 5, HGNC:13714) is a protein-coding gene on chromosome 19q13.33, encoding Calcium-binding protein 5 (Q9NP86). Inhibits calcium-dependent inactivation of L-type calcium channel and shifts voltage dependence of activation to more depolarized membrane potentials.

The product of this gene belongs to a subfamily of calcium binding proteins, which share similarity to calmodulin. Calcium binding proteins are an important component of calcium mediated cellular signal transduction. Expression of this gene is retina-specific. The mouse homolog of this protein has been shown to express in the inner nuclear layer of the retina, suggested its role in neuronal functioning. The specific function of this gene is unknown.

Source: NCBI Gene 56344 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_019855

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13714
Approved symbol	CABP5
Name	calcium binding protein 5
Location	19q13.33
Locus type	gene with protein product
Status	Approved
Aliases	CaBP3
Ensembl gene	ENSG00000105507
Ensembl biotype	protein_coding
OMIM	607315
Entrez	56344

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000293255, ENST00000602032

RefSeq mRNA: 1 — MANE Select: NM_019855 NM_019855

CCDS: CCDS12709

Canonical transcript exons

ENST00000293255 — 6 exons

Exon	Start	End
ENSE00000717850	48040605	48040748
ENSE00000717851	48039208	48039317
ENSE00001058735	48041573	48041603
ENSE00001132283	48034215	48034362
ENSE00001206737	48043860	48044079
ENSE00001316673	48029383	48030582

Expression profiles

Bgee: expression breadth broad, 37 present calls, max score 87.19.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2238 / max 163.2277, expressed in 10 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181806	0.1876	10
181808	0.0135	3
181807	0.0106	3
181805	0.0079	3
208883	0.0041	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	87.19	gold quality
mononuclear cell	CL:0000842	86.39	gold quality
leukocyte	CL:0000738	85.13	gold quality
granulocyte	CL:0000094	65.19	gold quality
cervix squamous epithelium	UBERON:0006922	63.41	gold quality
buccal mucosa cell	CL:0002336	62.02	silver quality
pancreatic ductal cell	CL:0002079	61.28	silver quality
hair follicle	UBERON:0002073	57.55	gold quality
blood	UBERON:0000178	56.86	gold quality
decidua	UBERON:0002450	56.55	gold quality
retina	UBERON:0000966	52.69	silver quality
pigmented layer of retina	UBERON:0001782	52.68	silver quality
cervix epithelium	UBERON:0004801	52.58	gold quality
epithelial cell of pancreas	CL:0000083	51.42	gold quality
male germ cell	CL:0000015	50.73	gold quality
sperm	CL:0000019	50.44	gold quality
oviduct epithelium	UBERON:0004804	50.44	gold quality
Brodmann (1909) area 46	UBERON:0006483	50.05	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
choroid plexus epithelium	UBERON:0003911	48.89	gold quality
myocardium	UBERON:0002349	48.87	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
quadriceps femoris	UBERON:0001377	48.77	gold quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality
vastus lateralis	UBERON:0001379	48.25	gold quality
left ventricle myocardium	UBERON:0006566	48.24	gold quality
orbitofrontal cortex	UBERON:0004167	48.20	gold quality
deltoid	UBERON:0001476	48.11	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting CABP5, 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-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-3140-5P	99.39	69.04	1136
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-488-5P	99.28	68.12	821
HSA-MIR-4795-5P	99.11	66.90	876
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-4695-5P	99.06	64.87	1151

Literature-anchored findings (GeneRIF, showing 1)

• the faster migrating Tg adduct C primarily engages the CaBP1/P5 oxidoreductase, whereas the slower migrating Tg adduct A primarily engages ERp72. (PMID:24599957)

Cross-species orthologs

16 orthologs

Organism	Symbol	Gene ID
danio_rerio	cabp5a	ENSDARG00000002576
danio_rerio	cabp5b	ENSDARG00000028485
mus_musculus	Cabp5	ENSMUSG00000005649
rattus_norvegicus	Cabp5	ENSRNOG00000014787
drosophila_melanogaster	TpnC4	FBGN0033027
drosophila_melanogaster	CG13526	FBGN0034774
drosophila_melanogaster	CG5024	FBGN0039373
drosophila_melanogaster	CG17770	FBGN0039374
drosophila_melanogaster	CG30378	FBGN0050378
caenorhabditis_elegans		WBGENE00000285
caenorhabditis_elegans		WBGENE00000287
caenorhabditis_elegans	pat-10	WBGENE00003934
caenorhabditis_elegans		WBGENE00006583
caenorhabditis_elegans		WBGENE00008453
caenorhabditis_elegans	F35C12.3	WBGENE00009408
caenorhabditis_elegans		WBGENE00015264

Paralogs (20): CABP7 (ENSG00000100314), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CETN3 (ENSG00000153140), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CABP2 (ENSG00000167791), CALML6 (ENSG00000169885), EFCAB3 (ENSG00000172421), EFCAB12 (ENSG00000172771), CABP4 (ENSG00000175544), CETN1 (ENSG00000177143), CALML3 (ENSG00000178363), CALML5 (ENSG00000178372), CALN1 (ENSG00000183166), CALM1 (ENSG00000198668), EFCAB2 (ENSG00000203666), EFCAB7 (ENSG00000203965), EFCAB9 (ENSG00000214360)

Protein

Protein identifiers

Calcium-binding protein 5 — Q9NP86 (reviewed: Q9NP86)

All UniProt accessions (1): Q9NP86

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits calcium-dependent inactivation of L-type calcium channel and shifts voltage dependence of activation to more depolarized membrane potentials. Involved in the transmission of light signals. May positively regulate neurotransmitter vesicle endocytosis and exocytosis in a salt-dependent manner. May play a role in the extension and network organization of neurites.

Subunit / interactions. Interacts with CACNA1C (via C-terminal CDB motif) in a calcium-dependent manner. Interacts with STXBP1. Interacts with MYO6.

Subcellular location. Cytoplasm.

Tissue specificity. Retina.

RefSeq proteins (1): NP_062829* (*=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
IPR043582	CaBP1/2/4/5	Family

Pfam: PF13499

UniProt features (24 total): binding site 14, sequence variant 5, domain 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NP86-F1	79.89	0.07

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): 120; 122; 124; 129; 155; 157; 159; 161; 166; 41; 43; 45 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 65 (showing top): GOBP_PHOTOTRANSDUCTION, MODULE_205, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, TGIF_01, GOBP_RESPONSE_TO_RADIATION, GOBP_DETECTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, MODULE_48, MODULE_95, MODULE_455, GOBP_RESPONSE_TO_LIGHT_STIMULUS, GOMF_CALCIUM_CHANNEL_REGULATOR_ACTIVITY

GO Biological Process (1): signal transduction (GO:0007165)

GO Molecular Function (4): calcium channel regulator activity (GO:0005246), calcium ion binding (GO:0005509), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
calcium channel activity	1
ion channel regulator activity	1
metal ion binding	1
binding	1
cation binding	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

1567 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CABP5	GRK5	P34947	616
CABP5	ZSWIM9	Q86XI8	518
CABP5	GRM6	O15303	487
CABP5	S100G	P29377	479
CABP5	RHO	P08100	471
CABP5	STXBP1	P61764	469
CABP5	PCP2	Q8IVA1	468
CABP5	VSX2	P58304	458
CABP5	MYO1C	O00159	440
CABP5	VSX1	Q9NZR4	430
CABP5	ARR3	P36575	420
CABP5	GNAT1	P11488	404
CABP5	ELSPBP1	Q96BH3	391
CABP5	ALPK1	Q96QP1	384
CABP5	GUCA1C	O95843	378

IntAct

130 interactions, top by confidence:

A	B	Type	Score
INCA1	CABP5	psi-mi:“MI:0915”(physical association)	0.830
CEP76	CABP5	psi-mi:“MI:0915”(physical association)	0.830
CABP5	INCA1	psi-mi:“MI:0915”(physical association)	0.830
CABP5	CEP76	psi-mi:“MI:0915”(physical association)	0.830
CABP5	ZKSCAN4	psi-mi:“MI:0915”(physical association)	0.780
ZKSCAN4	CABP5	psi-mi:“MI:0915”(physical association)	0.780
TCF4	CABP5	psi-mi:“MI:0915”(physical association)	0.740
CABP5	TCF4	psi-mi:“MI:0915”(physical association)	0.740
CABP5	IKZF3	psi-mi:“MI:0915”(physical association)	0.700
IKZF3	CABP5	psi-mi:“MI:0915”(physical association)	0.700
CABP5	REL	psi-mi:“MI:0915”(physical association)	0.560
REL	CABP5	psi-mi:“MI:0915”(physical association)	0.560
CABP5	ZNF664	psi-mi:“MI:0915”(physical association)	0.560
CABP5	ZNF559	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (46): CABP5 (Two-hybrid), CABP5 (Two-hybrid), CABP5 (Two-hybrid), CEP76 (Two-hybrid), ZKSCAN4 (Two-hybrid), INCA1 (Two-hybrid), TCF4 (Two-hybrid), INCA1 (Two-hybrid), CEP76 (Two-hybrid), CABP5 (Two-hybrid), CABP5 (Two-hybrid), CABP5 (Two-hybrid), CABP5 (Two-hybrid), PAX4 (Two-hybrid), LZTS2 (Two-hybrid)

ESM2 similar proteins: A0A125YHX7, O82018, O94739, P02597, P02598, P02599, P02605, P04353, P05419, P05932, P05933, P07462, P11118, P11120, P13868, P17928, P27161, P27163, P27166, P27482, P41040, P48976, P59220, P62150, P62199, P62200, P62201, P62202, P82160, P84339, P93171, Q03042, Q03509, Q0JNS6, Q16982, Q39752, Q41420, Q5U206, Q5XGC7, Q7DMN9

Diamond homologs: A8CEP3, D2DGW3, O16305, O60041, O88751, O94739, O96102, P02585, P02586, P02587, P02588, P02589, P02597, P02598, P02599, P04464, P05419, P05933, P06707, P06708, P06787, P07463, P10246, P11118, P11120, P11121, P15094, P15159, P18061, P20801, P23286, P24044, P25071, P27165, P27166, P29290, P29291, P47947, P47948, P47949

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1196 predictions. Top by Δscore:

Variant	Effect	Δscore
19:48030578:AAACT:A	acceptor_gain	1.0000
19:48030579:AACT:A	acceptor_gain	1.0000
19:48030581:CT:C	acceptor_gain	1.0000
19:48030581:CTCTG:C	acceptor_loss	1.0000
19:48030582:TC:T	acceptor_loss	1.0000
19:48030583:C:CC	acceptor_gain	1.0000
19:48030583:CTGCA:C	acceptor_loss	1.0000
19:48030584:T:G	acceptor_loss	1.0000
19:48034359:CAAA:C	acceptor_gain	1.0000
19:48034363:C:CC	acceptor_gain	1.0000
19:48039206:ACCT:A	donor_gain	1.0000
19:48039207:CCTC:C	donor_gain	1.0000
19:48039314:CCCA:C	acceptor_gain	1.0000
19:48039315:CCAC:C	acceptor_gain	1.0000
19:48039318:C:CC	acceptor_gain	1.0000
19:48040598:GACTC:G	donor_loss	1.0000
19:48040599:ACTC:A	donor_loss	1.0000
19:48040600:CTCA:C	donor_loss	1.0000
19:48040601:TCA:T	donor_loss	1.0000
19:48040602:CACGG:C	donor_loss	1.0000
19:48040603:A:AC	donor_gain	1.0000
19:48040603:A:C	donor_loss	1.0000
19:48040604:C:CA	donor_gain	1.0000
19:48040604:CG:C	donor_gain	1.0000
19:48040604:CGG:C	donor_gain	1.0000
19:48040604:CGGTT:C	donor_gain	1.0000
19:48043859:CCCG:C	donor_gain	1.0000
19:48043883:T:A	donor_gain	1.0000
19:48034358:TCAAA:T	acceptor_gain	0.9900
19:48034359:CAAAC:C	acceptor_gain	0.9900

AlphaMissense

1157 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:48034226:A:T	V162D	0.998
19:48039214:G:C	F114L	0.997
19:48039214:G:T	F114L	0.997
19:48039215:A:G	F114S	0.997
19:48039216:A:G	F114L	0.997
19:48040732:A:C	F37L	0.997
19:48040732:A:T	F37L	0.997
19:48040734:A:G	F37L	0.997
19:48034322:A:G	L130P	0.996
19:48034337:A:G	I125T	0.996
19:48039290:A:G	F89S	0.996
19:48040637:A:G	L69P	0.996
19:48040745:A:G	L33P	0.996
19:48030578:A:C	F167L	0.995
19:48030578:A:T	F167L	0.995
19:48030580:A:G	F167L	0.995
19:48034337:A:C	I125S	0.995
19:48039219:C:G	A113P	0.995
19:48040700:A:T	I48N	0.995
19:48040723:G:C	F40L	0.995
19:48040723:G:T	F40L	0.995
19:48040725:A:G	F40L	0.995
19:48040733:A:G	F37S	0.995
19:48040676:A:G	L56P	0.994
19:48039281:A:G	L92P	0.993
19:48040652:G:T	P64H	0.993
19:48040685:A:G	L53P	0.993
19:48034337:A:T	I125N	0.992
19:48039289:A:C	F89L	0.992
19:48039289:A:T	F89L	0.992

dbSNP variants (sampled 300 via entrez): RS1000148987 (19:48034951 T>A), RS1000194017 (19:48031817 C>T), RS1000244378 (19:48034769 C>T), RS1000303327 (19:48037398 A>G), RS1000377984 (19:48037621 C>A,T), RS1000493453 (19:48040116 T>G), RS1000646230 (19:48030974 T>C), RS1000664053 (19:48032167 T>C), RS1000693859 (19:48039039 G>A), RS1000887146 (19:48044476 G>T), RS1000973703 (19:48044269 T>C), RS1000976563 (19:48041654 T>C), RS1001232023 (19:48038794 T>A), RS1001323627 (19:48041808 C>T), RS1001365513 (19:48031530 A>C)

Disease associations

OMIM: gene MIM:607315 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST009700_9	Obesity (extreme)	6.000000e-06
GCST009701_7	Body mass index	5.000000e-06
GCST009733_121	Urinary metabolite levels in chronic kidney disease	4.000000e-20
GCST009733_203	Urinary metabolite levels in chronic kidney disease	6.000000e-15
GCST009733_213	Urinary metabolite levels in chronic kidney disease	4.000000e-31
GCST010002_57	Refractive error	1.000000e-27

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0005116	urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
daidzein	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
daidzin	affects cotreatment, increases expression	1
genistin	increases expression, affects cotreatment	1
glycitein	increases expression, affects cotreatment	1
cylindrospermopsin	increases expression	1
glycitin	affects cotreatment, increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Aflatoxin B1	increases methylation	1
Genistein	affects cotreatment, increases expression	1
Permethrin	affects response to substance	1

Clinical trials (associated diseases)

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