EFCAB12

gene
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Summary

EFCAB12 (EF-hand calcium binding domain 12, HGNC:28061) is a protein-coding gene on chromosome 3q21.3, encoding EF-hand calcium-binding domain-containing protein 12 (Q6NXP0).

Predicted to enable calcium ion binding activity.

Source: NCBI Gene 90288 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 104 total — 1 pathogenic
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_207307

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28061
Approved symbolEFCAB12
NameEF-hand calcium binding domain 12
Location3q21.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000172771
Ensembl biotypeprotein_coding
Entrez90288

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 retained_intron, 2 protein_coding

ENST00000503498, ENST00000503957, ENST00000505956, ENST00000514900

RefSeq mRNA: 1 — MANE Select: NM_207307 NM_207307

CCDS: CCDS54638

Canonical transcript exons

ENST00000505956 — 9 exons

ExonStartEnd
ENSE00002078715129401321129401851
ENSE00002319121129421367129421803
ENSE00003567465129402523129402579
ENSE00003571521129411158129411354
ENSE00003576447129415245129415401
ENSE00003597385129408645129408858
ENSE00003606408129418254129418448
ENSE00003671174129404250129404403
ENSE00003844630129428440129428636

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 97.10.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1949 / max 107.8840, expressed in 315 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
445191.1949315

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130297.10gold quality
bronchial epithelial cellCL:000232893.57gold quality
bronchusUBERON:000218592.42gold quality
mucosa of paranasal sinusUBERON:000503083.82gold quality
olfactory segment of nasal mucosaUBERON:000538683.55gold quality
oviduct epitheliumUBERON:000480482.51gold quality
fallopian tubeUBERON:000388980.21gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.50gold quality
adenohypophysisUBERON:000219676.33gold quality
pituitary glandUBERON:000000776.22gold quality
nasal cavity epitheliumUBERON:000538475.93gold quality
epithelium of nasopharynxUBERON:000195175.20silver quality
left testisUBERON:000453374.55gold quality
right testisUBERON:000453474.55gold quality
testisUBERON:000047373.53gold quality
caput epididymisUBERON:000435873.26gold quality
prostate glandUBERON:000236771.44gold quality
nucleus accumbensUBERON:000188271.12gold quality
hypothalamusUBERON:000189869.85gold quality
right lungUBERON:000216769.04gold quality
nasal cavity mucosaUBERON:000182668.70gold quality
tracheaUBERON:000312668.16silver quality
right lobe of liverUBERON:000111467.94gold quality
cerebellar hemisphereUBERON:000224567.55gold quality
right lobe of thyroid glandUBERON:000111967.45gold quality
cerebellar cortexUBERON:000212967.44gold quality
caudate nucleusUBERON:000187367.06gold quality
right hemisphere of cerebellumUBERON:001489066.88gold quality
cerebellumUBERON:000203766.84gold quality
kidney epitheliumUBERON:000481966.26gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting EFCAB12, 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-3924100.0072.092394
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-378G99.7164.901106
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-488-3P99.6168.791731
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-642A-5P99.5165.101152
HSA-MIR-366898.5268.76951
HSA-MIR-58198.3967.42835
HSA-MIR-4436B-3P98.2565.261494
HSA-MIR-6735-5P98.2465.361488
HSA-MIR-7843-5P98.1265.261421
HSA-MIR-876-5P97.9968.491345
HSA-MIR-4632-5P97.8265.381470
HSA-MIR-6879-5P97.7765.521521
HSA-MIR-432997.6866.261003
HSA-MIR-316796.8167.091236
HSA-MIR-2276-5P96.2765.85937

Cross-species orthologs

15 orthologs

OrganismSymbolGene ID
mus_musculusEfcab12ENSMUSG00000030321
rattus_norvegicusEfcab12ENSRNOG00000026176
drosophila_melanogasterTpnC4FBGN0033027
drosophila_melanogasterCG13526FBGN0034774
drosophila_melanogasterCG5024FBGN0039373
drosophila_melanogasterCG17770FBGN0039374
drosophila_melanogasterCG30378FBGN0050378
caenorhabditis_elegansWBGENE00000285
caenorhabditis_elegansWBGENE00000287
caenorhabditis_eleganspat-10WBGENE00003934
caenorhabditis_elegansWBGENE00006583
caenorhabditis_elegansWBGENE00008453
caenorhabditis_elegansF35C12.3WBGENE00009408
caenorhabditis_elegansWBGENE00015264
caenorhabditis_elegansWBGENE00019352

Paralogs (20): CABP7 (ENSG00000100314), CABP5 (ENSG00000105507), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CETN3 (ENSG00000153140), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CABP2 (ENSG00000167791), CALML6 (ENSG00000169885), EFCAB3 (ENSG00000172421), CABP4 (ENSG00000175544), CETN1 (ENSG00000177143), CALML3 (ENSG00000178363), CALML5 (ENSG00000178372), CALN1 (ENSG00000183166), CALM1 (ENSG00000198668), EFCAB2 (ENSG00000203666), EFCAB7 (ENSG00000203965), EFCAB9 (ENSG00000214360)

Protein

Protein identifiers

EF-hand calcium-binding domain-containing protein 12Q6NXP0 (reviewed: Q6NXP0)

All UniProt accessions (2): Q6NXP0, D6RFI2

RefSeq proteins (1): NP_997190* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002048EF_hand_domDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR042847EFC12Family

UniProt features (10 total): sequence variant 5, region of interest 2, chain 1, domain 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6NXP0-F165.480.08

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 (1): 212

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): chr3q21, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, FOXN3_TARGET_GENES, ZNF10_TARGET_GENES, ZNF92_TARGET_GENES, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, MIR488_3P, GSE8685_IL2_ACT_IL2_STARVED_VS_IL21_ACT_IL2_STARVED_CD4_TCELL_UP, GSE14026_TH1_VS_TH17_UP, BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_DN, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_CEREBRUM_ASTROCYTES

GO Biological Process (0):

GO Molecular Function (3): calcium ion binding (GO:0005509), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
metal ion binding1
binding1
cation binding1

Protein interactions and networks

STRING

326 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EFCAB12SLC68A1Q14CX5477
EFCAB12KHDC4Q7Z7F0462
EFCAB12MPV17L2Q567V2412
EFCAB12MRPS33Q9Y291409
EFCAB12UQCC1Q9NVA1399
EFCAB12CFAP61Q8NHU2392
EFCAB12WSCD2Q2TBF2386
EFCAB12PTPDC1A2A3K4378
EFCAB12DDX52Q9Y2R4375
EFCAB12WDPCPO95876372
EFCAB12CFAP65Q6ZU64370
EFCAB12CCDC92Q53HC0366
EFCAB12ITPK1Q13572359
EFCAB12LRRC47Q8N1G4359
EFCAB12NUCKS1Q9H1E3336

IntAct

5 interactions, top by confidence:

ABTypeScore
FHL3EFCAB12psi-mi:“MI:0915”(physical association)0.560
EFCAB12FHL3psi-mi:“MI:0915”(physical association)0.560
EFCAB12H1-2psi-mi:“MI:0915”(physical association)0.400

BioGRID (8): EFCAB12 (Two-hybrid), EFCAB12 (Synthetic Lethality), EFCAB12 (Biochemical Activity), EFCAB12 (Proximity Label-MS), EFCAB12 (Cross-Linking-MS (XL-MS)), EFCAB12 (Cross-Linking-MS (XL-MS)), EFCAB12 (Cross-Linking-MS (XL-MS)), EFCAB12 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A3Q1MT14, A4D263, A6NL82, A6QQL5, A8QW39, B0UXH9, B5X5D0, B9EJX3, E1B9R1, F1MMV1, Q148A4, Q1JPL0, Q2T9T0, Q32KQ1, Q32L72, Q32L77, Q32P67, Q3V0J4, Q5BN46, Q5NC57, Q5NC83, Q5SPV6, Q5SS90, Q5SVJ3, Q5VTT2, Q5VZQ5, Q66HC0, Q66HR9, Q6AYM0, Q6NXP0, Q6P3G4, Q6ZVS7, Q80X60, Q8CDT5, Q8CDU5, Q8N5S3, Q8N7U6, Q8N865

Diamond homologs: Q6NXP0, Q95LL8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance82
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4075854GRCh37/hg19 3q21.3-22.1(chr3:129108935-129214595)x1Pathogenic

SpliceAI

1947 predictions. Top by Δscore:

VariantEffectΔscore
3:129401848:CTTC:Cacceptor_gain1.0000
3:129401849:TTCC:Tacceptor_loss1.0000
3:129401852:C:CCacceptor_gain1.0000
3:129401852:CTGGA:Cacceptor_loss1.0000
3:129402493:T:TAdonor_gain1.0000
3:129404248:G:Cdonor_gain1.0000
3:129411153:GGTAC:Gdonor_loss1.0000
3:129411154:GTA:Gdonor_loss1.0000
3:129411155:TA:Tdonor_loss1.0000
3:129411156:A:ATdonor_loss1.0000
3:129411157:C:Adonor_loss1.0000
3:129411198:T:TAdonor_gain1.0000
3:129411362:C:CTacceptor_gain1.0000
3:129411363:A:Tacceptor_gain1.0000
3:129415243:A:ACdonor_gain1.0000
3:129415243:ACGCT:Adonor_gain1.0000
3:129415244:C:CCdonor_gain1.0000
3:129415244:CG:Cdonor_gain1.0000
3:129415244:CGCT:Cdonor_gain1.0000
3:129415244:CGCTC:Cdonor_gain1.0000
3:129415248:C:CAdonor_gain1.0000
3:129415400:ACCTG:Aacceptor_loss1.0000
3:129415401:CCT:Cacceptor_loss1.0000
3:129415403:T:Gacceptor_loss1.0000
3:129418252:A:ACdonor_gain1.0000
3:129418253:C:CCdonor_gain1.0000
3:129418253:CTG:Cdonor_gain1.0000
3:129421327:AAAC:Adonor_gain1.0000
3:129421365:AC:Adonor_gain1.0000
3:129421366:CC:Cdonor_gain1.0000

AlphaMissense

3783 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:129418273:A:GF221S0.976
3:129401722:G:CF530L0.975
3:129401722:G:TF530L0.975
3:129401724:A:GF530L0.975
3:129401797:G:CF505L0.967
3:129401797:G:TF505L0.967
3:129401799:A:GF505L0.967
3:129415352:A:GL244P0.964
3:129418272:G:CF221L0.964
3:129418272:G:TF221L0.964
3:129418274:A:GF221L0.964
3:129401796:A:GW506R0.957
3:129401796:A:TW506R0.957
3:129401723:A:GF530S0.946
3:129421480:A:GW125R0.941
3:129421480:A:TW125R0.941
3:129401794:C:AW506C0.935
3:129401794:C:GW506C0.935
3:129415394:A:TV230D0.931
3:129418354:A:GL194P0.929
3:129402537:A:CF482L0.928
3:129402537:A:TF482L0.928
3:129402539:A:GF482L0.928
3:129401771:A:GL514P0.925
3:129415364:A:TI240K0.922
3:129421727:G:CF42L0.922
3:129421727:G:TF42L0.922
3:129421729:A:GF42L0.922
3:129415325:A:CI253S0.918
3:129415290:A:GW265R0.915

dbSNP variants (sampled 300 via entrez): RS1000015940 (3:129421050 T>C), RS1000098522 (3:129428754 A>G,T), RS1000150307 (3:129417347 A>C), RS1000237120 (3:129422337 T>C), RS1000296692 (3:129416025 C>A,T), RS1000298775 (3:129410033 C>T), RS1000522124 (3:129411632 T>A), RS1000571706 (3:129404678 C>G), RS1000739340 (3:129407146 G>C,T), RS1001039614 (3:129411331 C>A,G,T), RS1001125354 (3:129404874 C>G,T), RS1001366304 (3:129412399 C>T), RS1001418693 (3:129412695 C>G), RS1001462267 (3:129406527 G>A,T), RS1001553716 (3:129430213 A>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:209850

GenCC curated gene-disease

Mondo (1): autism (MONDO:0005260)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000717Autism

GWAS associations

14 associations (top):

StudyTraitp-value
GCST002875_11Diisocyanate-induced asthma2.000000e-06
GCST005551_4Systemic sclerosis (anti-topoisomerase-positive)3.000000e-06
GCST005956_82Waist-to-hip ratio adjusted for BMI2.000000e-07
GCST005958_5Waist-to-hip ratio adjusted for BMI (age >50)4.000000e-10
GCST005962_16Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)2.000000e-11
GCST007483_52Waist-to-hip ratio adjusted for BMI (additive genetic model)8.000000e-17
GCST007487_16Waist-to-hip ratio adjusted for BMI (additive genetic model)2.000000e-18
GCST007500_19Waist-to-hip ratio adjusted for BMI (additive genetic model)8.000000e-18
GCST007502_15Waist-to-hip ratio adjusted for BMI (additive genetic model)5.000000e-19
GCST90020024_1254A body shape index4.000000e-13
GCST90020025_594Waist-to-hip ratio adjusted for BMI5.000000e-22
GCST90020027_371Waist-hip index2.000000e-21
GCST90020028_1841Hip circumference adjusted for BMI3.000000e-09
GCST90020029_1349Waist circumference adjusted for body mass index3.000000e-11

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate
EFO:0008537anti-topoisomerase-I-antibody-positive systemic scleroderma
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (1)

DescriptorNameTree numbers
D001321Autistic DisorderF03.625.164.113.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1decreases expression, decreases methylation, increases methylation3
Benzo(a)pyreneaffects methylation, decreases expression2
Tobacco Smoke Pollutionaffects expression, decreases expression2
triphenyl phosphateaffects expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
mancozebdecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
di-n-butylphosphoric acidaffects expression1
clothianidindecreases expression1
enzalutamidedecreases expression1
(+)-JQ1 compoundincreases expression1
Air Pollutantsincreases expression, increases abundance1
Lipopolysaccharidesaffects response to substance, increases expression1
Smokeincreases abundance, increases expression1
Dihydrotestosteroneincreases expression1
Cyclosporinedecreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00211796PHASE4COMPLETEDDivalproex Sodium ER in Adult Autism
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747PHASE4COMPLETEDMinocycline to Treat Childhood Regressive Autism
NCT00576732PHASE4COMPLETEDA Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753PHASE4COMPLETEDAtomoxetine, Placebo and Parent Management Training in Autism
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383PHASE4UNKNOWNTreatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977PHASE4UNKNOWNStudy to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925PHASE4UNKNOWNAn Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565PHASE4COMPLETEDDose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT00036231PHASE3TERMINATEDSynthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244PHASE3COMPLETEDSynthetic Human Secretin in Children With Autism
NCT00065884PHASE3UNKNOWNValproate Response in Aggressive Autistic Adolescents
NCT00065962PHASE3COMPLETEDSecretin for the Treatment of Autism
NCT00252603PHASE3COMPLETEDGalantamine Versus Placebo in Childhood Autism
NCT00346736PHASE3COMPLETEDUse of Acupuncture In Children With Autistic Spectrum Disorder
NCT00352248PHASE3COMPLETEDRandomized Controlled Trial of Acupuncture Versus Sham Acupuncture in Autistic Spectrum Disorder
NCT00352352PHASE3COMPLETEDUse of Acupuncture In Children With Autistic Spectrum Disorder
NCT00355329PHASE3COMPLETEDRandomized Control Trial of Using Tongue Acupuncture in Autistic Spectrum Disorder Using PET Scan for Clinical Correlation
NCT00498173PHASE3COMPLETEDEffectiveness of Atomoxetine in Treating ADHD Symptoms in Children and Adolescents With Autism
NCT00541346PHASE3COMPLETEDA Pilot Study of Daytrana TM in Children With Autism Co-Morbid for Attention Deficit Hyperactivity Disorder (ADHD) Symptoms

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.