EFHD1

gene
On this page

Also known as FLJ13612

Summary

EFHD1 (EF-hand domain family member D1, HGNC:29556) is a protein-coding gene on chromosome 2q37.1, encoding EF-hand domain-containing protein D1 (Q9BUP0). Acts as a calcium sensor for mitochondrial flash (mitoflash) activation, an event characterized by stochastic bursts of superoxide production.

This gene encodes a member of the EF-hand super family of calcium binding proteins, which are involved in a variety of cellular processes including mitosis, synaptic transmission, and cytoskeletal rearrangement. The protein encoded by this gene is composed of an N-terminal disordered region, proline-rich elements, two EF-hands, and a C-terminal coiled-coil domain. This protein has been shown to associate with the mitochondrial inner membrane, and in HeLa cells, acts as a novel mitochondrial calcium ion sensor for mitochondrial flash activation. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 80303 — RefSeq curated summary.

At a glance

  • GWAS associations: 17
  • Clinical variants (ClinVar): 37 total
  • MANE Select transcript: NM_025202

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29556
Approved symbolEFHD1
NameEF-hand domain family member D1
Location2q37.1
Locus typegene with protein product
StatusApproved
AliasesFLJ13612
Ensembl geneENSG00000115468
Ensembl biotypeprotein_coding
OMIM611617
Entrez80303

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 nonsense_mediated_decay

ENST00000264059, ENST00000409613, ENST00000409708, ENST00000410095, ENST00000427698, ENST00000442845, ENST00000865005, ENST00000865006

RefSeq mRNA: 3 — MANE Select: NM_025202 NM_001243252, NM_001308395, NM_025202

CCDS: CCDS2497, CCDS58755, CCDS82580

Canonical transcript exons

ENST00000264059 — 4 exons

ExonStartEnd
ENSE00000965612232681585232682776
ENSE00001029714232633604232634006
ENSE00003474969232662802232662949
ENSE00003474989232672309232672443

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 99.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.3562 / max 1154.6047, expressed in 932 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
2600327.2236917
260001.2823273
259990.6963182
260040.6634328
260020.259172
260060.137772
260010.058327
259980.035420

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
inferior olivary complexUBERON:000212799.55gold quality
dorsal motor nucleus of vagus nerveUBERON:000287099.27gold quality
C1 segment of cervical spinal cordUBERON:000646999.19gold quality
popliteal arteryUBERON:000225099.01gold quality
tibial arteryUBERON:000761099.01gold quality
spinal cordUBERON:000224098.90gold quality
right coronary arteryUBERON:000162598.86gold quality
aortaUBERON:000094798.84gold quality
ascending aortaUBERON:000149698.75gold quality
thoracic aortaUBERON:000151598.74gold quality
descending thoracic aortaUBERON:000234598.34gold quality
cranial nerve IIUBERON:000094198.32gold quality
substantia nigraUBERON:000203898.32gold quality
medial globus pallidusUBERON:000247798.30gold quality
globus pallidusUBERON:000187598.28gold quality
midbrainUBERON:000189198.19gold quality
inferior vagus X ganglionUBERON:000536398.16gold quality
left coronary arteryUBERON:000162698.02gold quality
metanephros cortexUBERON:001053397.98gold quality
renal medullaUBERON:000036297.93gold quality
CA1 field of hippocampusUBERON:000388197.91gold quality
adult mammalian kidneyUBERON:000008297.83gold quality
coronary arteryUBERON:000162197.78gold quality
lateral globus pallidusUBERON:000247697.67gold quality
subthalamic nucleusUBERON:000190697.66gold quality
amygdalaUBERON:000187697.65gold quality
putamenUBERON:000187497.62gold quality
hypothalamusUBERON:000189897.40gold quality
substantia nigra pars reticulataUBERON:000196697.39gold quality
blood vessel layerUBERON:000479797.38gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-MTAB-10885yes550.46
E-MTAB-3929yes186.56
E-MTAB-10287yes51.11
E-CURD-119yes47.49
E-GEOD-135922yes30.94
E-GEOD-84465yes10.06
E-GEOD-134144yes8.43
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HNF4A

miRNA regulators (miRDB)

49 targeting EFHD1, 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-211099.9666.681930
HSA-MIR-144-3P99.9473.982698
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-345-3P99.8970.231421
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-451799.7669.191867
HSA-MIR-149-3P99.7268.223963
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-371499.7170.742671
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-7-5P99.6770.531809
HSA-MIR-651-5P99.6468.491104
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-312399.4767.152693
HSA-MIR-127599.4767.902749
HSA-MIR-431699.3765.751360
HSA-MIR-568399.3668.592083
HSA-MIR-431199.3170.473041
HSA-MIR-149-5P99.2567.161315
HSA-MIR-491-5P99.1365.981468
HSA-MIR-93598.8269.361072
HSA-MIR-16-1-3P98.7069.231538
HSA-MIR-6840-3P98.6865.951923
HSA-MIR-2467-3P98.6567.181969

Literature-anchored findings (GeneRIF, showing 4)

  • Cloning of novel mouse genes associated with neuronal function, including Efhd1. (PMID:12270117)
  • detection of methylation of PPP1R3C alone or in combination with EFHD1 in plasma DNA showed high sensitivity and specificity in CRC detection, and may be useful detection method for CRC, especially for early-stage CRCs. (PMID:24861485)
  • EFHD1 functions as a novel mitochondrial Ca(2+) sensor underlying Ca(2+)-dependent activation of mitoflashes (PMID:26975899)
  • EFHD1, a novel mitochondrial regulator of tumor metastasis in clear cell renal cell carcinoma. (PMID:36747492)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioefhd1ENSDARG00000043446
mus_musculusEfhd1ENSMUSG00000026255
rattus_norvegicusEfhd1ENSRNOG00000015596
drosophila_melanogasterSwip-1FBGN0032731
drosophila_melanogasterCG14861FBGN0038280
caenorhabditis_elegansWBGENE00012980

Paralogs (1): EFHD2 (ENSG00000142634)

Protein

Protein identifiers

EF-hand domain-containing protein D1Q9BUP0 (reviewed: Q9BUP0)

Alternative names: EF-hand domain-containing protein 1, Swiprosin-2

All UniProt accessions (4): C9JTV4, Q9BUP0, H7C0I0, Q8WYH2

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a calcium sensor for mitochondrial flash (mitoflash) activation, an event characterized by stochastic bursts of superoxide production. May play a role in neuronal differentiation.

Subcellular location. Mitochondrion inner membrane.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BUP0-11yes
Q9BUP0-22

RefSeq proteins (3): NP_001230181, NP_001295324, NP_079478* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002048EF_hand_domDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR040365EFHD1/2Family

Pfam: PF13499

UniProt features (20 total): binding site 8, mutagenesis site 4, domain 2, chain 1, modified residue 1, splice variant 1, sequence variant 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BUP0-F178.100.25

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 (8): 143; 145; 150; 103; 107; 114; 139; 141

Post-translational modifications (1): 201

Mutagenesis-validated functional residues (4):

PositionPhenotype
103in mtefhd1; abolished ability to enhance mitoflash activity; when associated with k-114; a-139 and k-150.
114in mtefhd1; abolished ability to enhance mitoflash activity; when associated with a-103; a-139 and k-150.
139in mtefhd1; abolished ability to enhance mitoflash activity; when associated with a-103; k-114 and k-150.
150in mtefhd1; abolished ability to enhance mitoflash activity; when associated with a-103; k-114 and a-139.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 174 (showing top): PAX4_01, PEREZ_TP63_TARGETS, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_NEUROGENESIS, GOBP_HYPEROSMOTIC_RESPONSE, LUCAS_HNF4A_TARGETS_UP, SRF_Q5_01, SRF_C, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, RAMALHO_STEMNESS_DN, GOBP_RESPONSE_TO_SALT_STRESS, TCF11_01, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6

GO Biological Process (2): neuron projection development (GO:0031175), regulation of cellular hyperosmotic salinity response (GO:1900069)

GO Molecular Function (4): calcium ion binding (GO:0005509), calcium ion sensor activity (GO:0061891), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
neuron development1
plasma membrane bounded cell projection organization1
cellular hyperosmotic salinity response1
regulation of cellular response to osmotic stress1
regulation of response to salt stress1
metal ion binding1
calcium ion binding1
metal ion sensor activity1
binding1
cation binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
cellular anatomical structure1

Protein interactions and networks

STRING

1010 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EFHD1RHAGQ02094800
EFHD1ERMNQ8TAM6474
EFHD1SLC24A1O60721447
EFHD1TEX44Q53QW1421
EFHD1RRHO14718398
EFHD1OPN4Q9UHM6380
EFHD1RHOP08100379
EFHD1OPN3Q9H1Y3378
EFHD1OPN1SWP03999361
EFHD1ITSN1Q15811359
EFHD1OPN5Q6U736348
EFHD1TRIP12Q14669347
EFHD1EPS8L1Q8TE68329
EFHD1CYP27C1Q4G0S4323
EFHD1EFCC1Q9HA90320

IntAct

62 interactions, top by confidence:

ABTypeScore
EXOC6BEXOC5psi-mi:“MI:0914”(association)0.790
CEP164TTBK2psi-mi:“MI:0914”(association)0.680
ANXA9PPLpsi-mi:“MI:0914”(association)0.660
CAPZA2CNOT1psi-mi:“MI:0914”(association)0.640
G2E3SPECC1Lpsi-mi:“MI:0914”(association)0.560
ZIC2EFHD1psi-mi:“MI:0915”(physical association)0.560
MAS1POTEFpsi-mi:“MI:0914”(association)0.530
FSD1UBFD1psi-mi:“MI:0914”(association)0.530
DUSP10ACTBpsi-mi:“MI:0914”(association)0.530
OXNAD1HSPD1psi-mi:“MI:0914”(association)0.530
PPIAL4GACTBpsi-mi:“MI:0914”(association)0.530
NDNFEFHD1psi-mi:“MI:0915”(physical association)0.400
EFHD1PSEN1psi-mi:“MI:0915”(physical association)0.370
NS1SAC3D1psi-mi:“MI:0914”(association)0.350
PB2HAX1psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
PPIAL4GPPIAL4Dpsi-mi:“MI:0914”(association)0.350
FOXP2DUSP14psi-mi:“MI:0914”(association)0.350
CPLX4HSPA8psi-mi:“MI:0914”(association)0.350
S100A8SMTNL2psi-mi:“MI:0914”(association)0.350
OCIAD1NDUFS8psi-mi:“MI:0914”(association)0.350
PHYHIPLATP5F1Bpsi-mi:“MI:0914”(association)0.350
ADCK2SLC25A5psi-mi:“MI:0914”(association)0.350
PTPMT1NDUFAB1psi-mi:“MI:0914”(association)0.350
CTBP1TAF15psi-mi:“MI:0914”(association)0.350

BioGRID (95): EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), EFHD1 (Affinity Capture-RNA), EFHD1 (Affinity Capture-MS), TCHH (Affinity Capture-MS), KRT33B (Affinity Capture-MS), EFHD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I6A2H6, A2VEI2, A4IG32, A4IHK8, A5D7A0, D2HZB0, D4A1F2, E9Q4Z2, F1MF74, O00763, O08874, O14795, O94851, P23092, Q05AA6, Q08BI9, Q13474, Q17QM6, Q3TWN3, Q4FZY0, Q4KUS2, Q4V8B2, Q5E9V1, Q5R9G1, Q5RDI4, Q5U2P1, Q5ZJT0, Q62768, Q62769, Q69ZT9, Q6DFA1, Q86XE3, Q8BHD4, Q8BML1, Q8IWE4, Q8K0V2, Q8WN03, Q96C19, Q9BQI0, Q9BUP0

Diamond homologs: A5D7A0, O70200, O81092, P04112, P04113, P05944, P29289, P54680, P55008, P55009, P81076, Q09011, Q11083, Q17QM6, Q32LE3, Q4FZY0, Q54QX0, Q5RDI4, Q5TM25, Q8VWY7, Q96C19, Q9AWK2, Q9BDK2, Q9BQI0, Q9BUP0, Q9D4J1, Q9D8Y0, Q9EQX4, Q9SRP7, Q9VJ26, O60041, O96102, P06787, P14533, P25071, P80322, Q09665, Q12798, Q9XZP2, A4IF97

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance30
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

728 predictions. Top by Δscore:

VariantEffectΔscore
2:232634007:G:GGdonor_gain1.0000
2:232662908:G:GTdonor_gain1.0000
2:232662935:C:Gdonor_gain1.0000
2:232662947:G:GTdonor_gain1.0000
2:232662947:G:Tdonor_gain1.0000
2:232672304:T:Aacceptor_gain1.0000
2:232672307:A:AGacceptor_gain1.0000
2:232672308:G:GAacceptor_gain1.0000
2:232672308:GT:Gacceptor_gain1.0000
2:232672308:GTT:Gacceptor_gain1.0000
2:232672308:GTTC:Gacceptor_gain1.0000
2:232672308:GTTCC:Gacceptor_gain1.0000
2:232672419:TGCC:Tdonor_gain1.0000
2:232672441:AAGG:Adonor_loss1.0000
2:232672444:G:Adonor_loss1.0000
2:232672445:T:Gdonor_loss1.0000
2:232633984:G:GTdonor_gain0.9900
2:232633991:A:Tdonor_gain0.9900
2:232634003:AACT:Adonor_gain0.9900
2:232634003:AACTG:Adonor_loss0.9900
2:232634004:ACT:Adonor_gain0.9900
2:232634004:ACTG:Adonor_loss0.9900
2:232634005:CT:Cdonor_gain0.9900
2:232634005:CTGT:Cdonor_loss0.9900
2:232634006:TGTG:Tdonor_loss0.9900
2:232634007:GT:Gdonor_loss0.9900
2:232634008:T:Gdonor_loss0.9900
2:232662791:T:Aacceptor_gain0.9900
2:232662796:CTGCA:Cacceptor_loss0.9900
2:232662797:TGCA:Tacceptor_loss0.9900

AlphaMissense

1570 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:232662843:T:CL115P0.991
2:232633999:T:CF99L0.989
2:232634001:C:AF99L0.989
2:232634001:C:GF99L0.989
2:232662891:T:CL131P0.989
2:232672309:T:CF151L0.987
2:232672311:C:AF151L0.987
2:232672311:C:GF151L0.987
2:232662856:G:AM119I0.984
2:232662856:G:CM119I0.984
2:232662856:G:TM119I0.984
2:232672432:T:CF192L0.984
2:232672434:T:AF192L0.984
2:232672434:T:GF192L0.984
2:232634000:T:CF99S0.983
2:232662847:G:CK116N0.983
2:232662847:G:TK116N0.983
2:232662883:C:AH128Q0.983
2:232662883:C:GH128Q0.983
2:232672321:T:CF155L0.982
2:232672323:C:AF155L0.982
2:232672323:C:GF155L0.982
2:232672310:T:CF151S0.981
2:232662881:C:GH128D0.979
2:232662828:T:AI110N0.978
2:232672313:T:CL152P0.977
2:232672438:G:CA194P0.977
2:232662936:T:AL146H0.974
2:232662891:T:AL131Q0.973
2:232672330:G:CA158P0.971

dbSNP variants (sampled 300 via entrez): RS1000040665 (2:232635072 G>C,T), RS1000117442 (2:232646963 T>C), RS1000129451 (2:232643410 A>G), RS1000141048 (2:232632328 A>T), RS1000238959 (2:232663802 A>G), RS1000262827 (2:232670924 T>C), RS1000286905 (2:232630782 A>G), RS1000317007 (2:232682380 A>G), RS1000334173 (2:232610616 G>A,T), RS1000410847 (2:232643167 A>G), RS1000444337 (2:232649446 T>C), RS1000479538 (2:232647964 G>A), RS1000483506 (2:232636468 G>A), RS1000518893 (2:232680832 T>A,G), RS1000551012 (2:232670772 A>G)

Disease associations

OMIM: gene MIM:611617 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

StudyTraitp-value
GCST001277_12Liver enzyme levels (gamma-glutamyl transferase)1.000000e-09
GCST002539_44Schizophrenia2.000000e-12
GCST005998_8Alanine transaminase levels2.000000e-16
GCST005999_7Aspartate aminotransferase levels6.000000e-09
GCST006019_46Gamma glutamyl transferase levels5.000000e-16
GCST006803_9Schizophrenia4.000000e-16
GCST007201_285Schizophrenia6.000000e-09
GCST010002_411Refractive error1.000000e-123
GCST010479_63Coronary artery disease4.000000e-08
GCST011349_43Gamma glutamyl transferase levels6.000000e-14
GCST011352_19Alanine aminotransferase levels2.000000e-20
GCST90011898_95Alanine aminotransferase levels4.000000e-50
GCST90011899_31Aspartate aminotransferase levels2.000000e-23
GCST90013405_68Liver enzyme levels (alanine transaminase)5.000000e-53
GCST90013407_14Liver enzyme levels (gamma-glutamyl transferase)6.000000e-49
GCST90013663_72Alanine aminotransferase levels3.000000e-43
GCST90013664_102Aspartate aminotransferase levels4.000000e-17

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004532serum gamma-glutamyl transferase measurement
EFO:0004736aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression6
sodium arseniteaffects methylation, affects cotreatment, decreases expression, increases abundance, increases expression (+1 more)4
bisphenol Adecreases expression, decreases methylation3
Resveratrolaffects cotreatment, decreases expression2
Benzo(a)pyreneaffects methylation, increases methylation2
Cisplatinaffects expression, decreases expression2
Silicon Dioxidedecreases expression, decreases methylation2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Genisteinaffects cotreatment, affects expression, increases expression, increases reaction2
aristolochic acid Idecreases expression1
dicrotophosincreases expression1
2,4,6-tribromophenolincreases expression1
daidzeinaffects cotreatment, affects expression1
methylmercuric chloridedecreases expression1
propionaldehydeincreases expression1
decabromobiphenyl etherdecreases expression1
daidzinaffects expression, affects cotreatment1
sulforaphanedecreases expression1
butyraldehydeincreases expression1
tetrabromobisphenol Aincreases expression1
tobacco tardecreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
benzo(e)pyrenedecreases methylation1
potassium chromate(VI)increases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactonedecreases expression, affects cotreatment1
genistinaffects cotreatment, affects expression1
pentanalincreases expression1
cordycepindecreases expression1
perfluorooctane sulfonic aciddecreases expression1
glyciteinaffects cotreatment, affects expression1

Clinical trials (associated diseases)

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

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