CAMTA2

Summary

CAMTA2 (calmodulin binding transcription activator 2, HGNC:18807) is a protein-coding gene on chromosome 17p13.2, encoding Calmodulin-binding transcription activator 2 (O94983). Transcription activator.

The protein encoded by this gene is a member of the calmodulin-binding transcription activator protein family. Members of this family share a common domain structure that consists of a transcription activation domain, a DNA-binding domain, and a calmodulin-binding domain. The encoded protein may be a transcriptional coactivator of genes involved in cardiac growth. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 23125 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 239 total
• MANE Select transcript: NM_015099

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18807
Approved symbol	CAMTA2
Name	calmodulin binding transcription activator 2
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0909
Ensembl gene	ENSG00000108509
Ensembl biotype	protein_coding
OMIM	611508
Entrez	23125

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 20 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000348066, ENST00000361571, ENST00000381311, ENST00000414043, ENST00000571831, ENST00000572192, ENST00000572326, ENST00000572543, ENST00000573004, ENST00000574442, ENST00000574606, ENST00000574951, ENST00000575192, ENST00000575365, ENST00000575580, ENST00000576872, ENST00000892492, ENST00000892493, ENST00000892494, ENST00000892495, ENST00000892496, ENST00000892497, ENST00000892498, ENST00000892499, ENST00000892500, ENST00000935711, ENST00000935712, ENST00000943393, ENST00000943394, ENST00000943395

RefSeq mRNA: 4 — MANE Select: NM_015099 NM_001171166, NM_001171167, NM_001171168, NM_015099

CCDS: CCDS11063, CCDS54071, CCDS54072, CCDS54073

Canonical transcript exons

ENST00000348066 — 23 exons

Exon	Start	End
ENSE00000675648	4985880	4985983
ENSE00000675747	4982089	4982160
ENSE00001699395	4969500	4969520
ENSE00001945977	4987593	4987675
ENSE00003469915	4967997	4968819
ENSE00003489269	4981678	4981831
ENSE00003518756	4969902	4970085
ENSE00003520072	4972769	4972991
ENSE00003544657	4973585	4973769
ENSE00003556672	4973175	4973253
ENSE00003566450	4982757	4982892
ENSE00003571400	4970340	4970536
ENSE00003576683	4969630	4969701
ENSE00003577253	4969150	4969337
ENSE00003585015	4977058	4977192
ENSE00003604364	4972232	4972536
ENSE00003611195	4979684	4980621
ENSE00003616746	4974385	4974500
ENSE00003619657	4978504	4978630
ENSE00003628243	4986192	4986286
ENSE00003637595	4968907	4968981
ENSE00003651619	4982976	4983043
ENSE00003679248	4981225	4981359

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 98.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.0753 / max 580.5247, expressed in 1807 samples.

FANTOM5 promoters (18 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164008	8.8957	1745
163995	6.8817	955
163994	4.2394	926
163996	4.0199	838
164007	2.7120	1263
163998	2.5444	836
163991	1.0341	494
163990	0.7004	391
164002	0.4337	193
164006	0.4257	187

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	98.60	gold quality
cerebellar hemisphere	UBERON:0002245	98.34	gold quality
right frontal lobe	UBERON:0002810	98.30	gold quality
cerebellar cortex	UBERON:0002129	98.23	gold quality
anterior cingulate cortex	UBERON:0009835	97.54	gold quality
adenohypophysis	UBERON:0002196	97.34	gold quality
cingulate cortex	UBERON:0003027	97.34	gold quality
cerebellum	UBERON:0002037	96.52	gold quality
mucosa of stomach	UBERON:0001199	96.36	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.33	gold quality
prefrontal cortex	UBERON:0000451	96.32	gold quality
lower esophagus mucosa	UBERON:0035834	96.25	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.03	gold quality
mucosa of transverse colon	UBERON:0004991	96.01	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.77	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.73	gold quality
lower esophagus	UBERON:0013473	95.72	gold quality
apex of heart	UBERON:0002098	95.62	gold quality
metanephros cortex	UBERON:0010533	95.57	gold quality
gastrocnemius	UBERON:0001388	95.35	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.14	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.13	gold quality
pituitary gland	UBERON:0000007	95.11	gold quality
body of uterus	UBERON:0009853	95.09	gold quality
body of stomach	UBERON:0001161	94.94	gold quality
caudate nucleus	UBERON:0001873	94.91	gold quality
transverse colon	UBERON:0001157	94.88	gold quality
upper lobe of left lung	UBERON:0008952	94.82	gold quality
ascending aorta	UBERON:0001496	94.80	gold quality
thoracic aorta	UBERON:0001515	94.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.13

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F6

miRNA regulators (miRDB)

35 targeting CAMTA2, 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-4262	100.00	73.26	3931
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-567	99.63	68.57	1219
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-5697	99.39	67.74	1249
HSA-MIR-4641	99.28	66.64	744
HSA-MIR-4687-5P	99.14	66.26	488
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-6754-3P	98.84	66.60	889
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-6837-3P	98.42	66.71	1149
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-299-3P	97.73	66.67	773
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-939-5P	97.10	65.80	1579

Literature-anchored findings (GeneRIF, showing 1)

• Mutation of CAMTA2 resulting in post-transcriptional inhibition of its own gene activity likely underlies a novel syndromic tremulous dystonia. (PMID:29110692)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	camta2	ENSDARG00000092799
		ENSDARG00000100769
mus_musculus	Camta2	ENSMUSG00000040712
rattus_norvegicus	Camta2	ENSRNOG00000004283

Paralogs (1): CAMTA1 (ENSG00000171735)

Protein

Protein identifiers

Calmodulin-binding transcription activator 2 — O94983 (reviewed: O94983)

All UniProt accessions (6): O94983, B7ZM30, I3L146, I3L2A1, I3L3V0, I3L3W6

UniProt curated annotations — full annotation on UniProt →

Function. Transcription activator. May act as tumor suppressor.

Subunit / interactions. May interact with calmodulin.

Subcellular location. Nucleus.

Tissue specificity. Detected in brain. Expressed at constant levels throughout the cell cycle in neuroblastoma cell lines.

Similarity. Belongs to the CAMTA family.

Isoforms (6)

UniProt ID	Names	Canonical?
O94983-1	1	yes
O94983-2	2
O94983-3	3
O94983-4	4
O94983-5	5
O94983-6	6

RefSeq proteins (4): NP_001164637, NP_001164638, NP_001164639, NP_055914* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002909	IPT_dom	Domain
IPR005559	CG-1_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR014756	Ig_E-set	Homologous_superfamily
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily

Pfam: PF01833, PF03859

UniProt features (34 total): compositionally biased region 7, splice variant 6, region of interest 5, sequence conflict 5, domain 3, repeat 3, sequence variant 2, chain 1, short sequence motif 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O94983-F1	60.82	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): AREB6_03, AP2_Q3, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, GOBP_MUSCLE_ADAPTATION, GOBP_MUSCLE_HYPERTROPHY, GOBP_MUSCLE_SYSTEM_PROCESS, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, MARTIN_INTERACT_WITH_HDAC, GOBP_STRIATED_MUSCLE_ADAPTATION, AP2_Q6_01, GOMF_CHROMATIN_BINDING, SPZ1_01, ER_Q6_02, GOMF_HISTONE_DEACETYLASE_BINDING, MZF1_02

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), cardiac muscle hypertrophy in response to stress (GO:0014898), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): chromatin binding (GO:0003682), double-stranded DNA binding (GO:0003690), transcription coregulator activity (GO:0003712), transcription coactivator activity (GO:0003713), histone deacetylase binding (GO:0042826), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	2
positive regulation of DNA-templated transcription	2
binding	2
DNA binding	2
regulation of DNA-templated transcription	1
muscle hypertrophy in response to stress	1
cardiac muscle hypertrophy	1
cardiac muscle adaptation	1
regulation of transcription by RNA polymerase II	1
transcription regulator activity	1
transcription coregulator activity	1
enzyme binding	1
nucleic acid binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

600 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CAMTA2	CALM1	P02593	645
CAMTA2	CALML3	P27482	628
CAMTA2	CALML5	Q9NZT1	628
CAMTA2	CALML6	Q8TD86	627
CAMTA2	CALML4	Q96GE6	627
CAMTA2	NPPA	P01160	605
CAMTA2	NKX2-5	P52952	560
CAMTA2	ANK1	P16157	517
CAMTA2	ANK2	Q01484	508
CAMTA2	ANK3	Q12955	507
CAMTA2	PRKD1	Q15139	496
CAMTA2	CAMTA1	Q9Y6Y1	487
CAMTA2	HDAC4	P56524	485
CAMTA2	HDAC9	Q9UKV0	477
CAMTA2	ZNF628	Q5EBL2	456

IntAct

15 interactions, top by confidence:

A	B	Type	Score
	CAMTA2	psi-mi:“MI:0914”(association)	0.460
CAMTA2	H2AC21	psi-mi:“MI:0915”(physical association)	0.400
CAMTA2	Nkx2-5	psi-mi:“MI:0915”(physical association)	0.400
	CAMTA2	psi-mi:“MI:0915”(physical association)	0.370
CAMTA2		psi-mi:“MI:0915”(physical association)	0.370
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
CAMTA2	PPP2R1A	psi-mi:“MI:0914”(association)	0.350
NKX2-5	CAMTA2	psi-mi:“MI:0403”(colocalization)	0.270
	CAMTA2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (26): CAMTA2 (Two-hybrid), CAMTA2 (Two-hybrid), FAM192A (Affinity Capture-MS), PSME3 (Affinity Capture-MS), FAM192A (Affinity Capture-MS), PSME3 (Affinity Capture-MS), CAMTA2 (Two-hybrid), CALM2 (Two-hybrid), CALM3 (Two-hybrid), MEMO1 (Two-hybrid), ZNF483 (Two-hybrid), MAGEA6 (Two-hybrid), CALM1 (Two-hybrid), CAMTA2 (Affinity Capture-RNA), CAMTA2 (Two-hybrid)

ESM2 similar proteins: A0JNI1, E9Q0S6, O94983, O95402, P80192, Q08AE8, Q1JQA8, Q1LZH7, Q28DG6, Q3B7I8, Q3KPL3, Q3U1V8, Q4VAC9, Q53LP3, Q5BJT1, Q5DU25, Q5HZA4, Q5JU85, Q5M836, Q5PQ30, Q5RBI7, Q5REP3, Q5XG99, Q5ZKK0, Q69YU3, Q6DCC7, Q6DEF4, Q6IPM2, Q6IQA2, Q6P606, Q76G19, Q7TSI1, Q7Z3D4, Q80Y50, Q86UU1, Q8BL43, Q8BY98, Q8C0J6, Q8CC84, Q8IV50

Diamond homologs: A2A891, H2KY84, O23463, O94983, Q6NPP4, Q7XHR2, Q80Y50, Q8GSA7, Q9FY74, Q9FYG2, Q9LSP8, Q9Y6Y1, P62294, Q10728, Q9DBR7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	189
Likely benign	9
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

3660 predictions. Top by Δscore:

Variant	Effect	Δscore
17:4968817:ATCC:A	acceptor_loss	1.0000
17:4968819:CCTGC:C	acceptor_loss	1.0000
17:4968820:CTGC:C	acceptor_loss	1.0000
17:4968821:T:A	acceptor_loss	1.0000
17:4968902:AGTAC:A	donor_loss	1.0000
17:4968903:GTA:G	donor_loss	1.0000
17:4968904:TA:T	donor_loss	1.0000
17:4968978:GCCT:G	acceptor_gain	1.0000
17:4968979:CCTC:C	acceptor_gain	1.0000
17:4968980:CT:C	acceptor_gain	1.0000
17:4968982:C:CC	acceptor_gain	1.0000
17:4968985:G:C	acceptor_gain	1.0000
17:4968985:G:GC	acceptor_gain	1.0000
17:4969144:CCCTA:C	donor_loss	1.0000
17:4969145:CCTA:C	donor_loss	1.0000
17:4969146:CTA:C	donor_loss	1.0000
17:4969147:TA:T	donor_loss	1.0000
17:4969148:A:AC	donor_gain	1.0000
17:4969148:ACTTG:A	donor_loss	1.0000
17:4969149:C:CA	donor_loss	1.0000
17:4969149:C:CC	donor_gain	1.0000
17:4969149:CTTG:C	donor_gain	1.0000
17:4969178:T:TA	donor_gain	1.0000
17:4969333:GCAAA:G	acceptor_gain	1.0000
17:4969334:CAAA:C	acceptor_gain	1.0000
17:4969334:CAAAC:C	acceptor_gain	1.0000
17:4969335:AAA:A	acceptor_gain	1.0000
17:4969336:AA:A	acceptor_gain	1.0000
17:4969337:AC:A	acceptor_loss	1.0000
17:4969338:C:CC	acceptor_gain	1.0000

AlphaMissense

7713 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:4968925:A:G	L1176P	1.000
17:4968927:G:C	F1175L	1.000
17:4968927:G:T	F1175L	1.000
17:4968928:A:C	F1175C	1.000
17:4968928:A:G	F1175S	1.000
17:4968929:A:G	F1175L	1.000
17:4968937:A:C	I1172S	1.000
17:4968937:A:G	I1172T	1.000
17:4968937:A:T	I1172N	1.000
17:4969228:A:C	I1131S	1.000
17:4969228:A:G	I1131T	1.000
17:4969228:A:T	I1131N	1.000
17:4969237:G:T	A1128D	1.000
17:4969257:A:C	F1121L	1.000
17:4969257:A:T	F1121L	1.000
17:4969258:A:G	F1121S	1.000
17:4969259:A:G	F1121L	1.000
17:4969284:G:C	F1112L	1.000
17:4969284:G:T	F1112L	1.000
17:4969285:A:G	F1112S	1.000
17:4969286:A:G	F1112L	1.000
17:4969297:A:G	I1108T	1.000
17:4969297:A:T	I1108N	1.000
17:4969300:A:G	L1107P	1.000
17:4969306:G:T	A1105D	1.000
17:4969307:C:G	A1105P	1.000
17:4969633:C:A	K1086N	1.000
17:4969633:C:G	K1086N	1.000
17:4969647:A:C	Y1082D	1.000
17:4969658:A:T	I1078N	1.000

dbSNP variants (sampled 300 via entrez): RS1000008477 (17:4982968 T>C,G), RS1000064517 (17:4975692 A>T), RS1000096604 (17:4975935 G>A,T), RS1000191463 (17:4986832 A>C), RS1000248186 (17:4970591 A>C), RS1000443242 (17:4983329 C>G), RS1000453724 (17:4987266 G>A), RS1000456742 (17:4967579 G>A,C), RS1000714376 (17:4970855 G>A), RS1000819683 (17:4979898 G>A), RS1000880987 (17:4974967 G>C,T), RS1001058184 (17:4968892 A>G,T), RS1001161052 (17:4968314 C>G), RS1001194001 (17:4988534 G>A,T), RS1001201473 (17:4968774 C>G,T)

Disease associations

OMIM: gene MIM:611508 | disease phenotypes: MIM:614756

GenCC curated gene-disease

Mondo (1): cerebellar dysfunction with variable cognitive and behavioral abnormalities (MONDO:0013886)

Orphanet (1): Non-progressive cerebellar ataxia with intellectual disability (Orphanet:314647)

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005580_15	Intraocular pressure	1.000000e-14
GCST005580_22	Intraocular pressure	3.000000e-14
GCST90013442_27	Keratoconus	2.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	3
Air Pollutants	increases expression, affects expression, increases abundance	2
Tretinoin	increases expression	2
Valproic Acid	increases expression, increases methylation	2
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
terbufos	increases methylation	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
tamibarotene	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Estradiol	affects cotreatment, decreases expression, increases expression	1
Ozone	increases abundance, affects expression	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	increases expression	1

Clinical trials (associated diseases)

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