EFCAB3

Summary

EFCAB3 (EF-hand calcium binding domain 3, HGNC:26379) is a protein-coding gene on chromosome 17q23.2, encoding EF-hand calcium-binding domain-containing protein 3 (Q8N7B9).

Predicted to enable calcium ion binding activity.

Source: NCBI Gene 146779 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 54 total — 1 likely-pathogenic
• MANE Select transcript: NM_173503

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26379
Approved symbol	EFCAB3
Name	EF-hand calcium binding domain 3
Location	17q23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25818
Ensembl gene	ENSG00000172421
Ensembl biotype	protein_coding
OMIM	619567
Entrez	146779

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000305286, ENST00000450662, ENST00000518576, ENST00000520404, ENST00000635817, ENST00000636041

RefSeq mRNA: 2 — MANE Select: NM_173503 NM_001144933, NM_173503

CCDS: CCDS11632, CCDS45751

Canonical transcript exons

ENST00000305286 — 10 exons

Exon	Start	End
ENSE00001181206	62416003	62416480
ENSE00001181211	62407028	62407212
ENSE00001181223	62393573	62393644
ENSE00001181228	62391822	62391965
ENSE00001181235	62387340	62387416
ENSE00001181237	62406480	62406673
ENSE00001250797	62380553	62380613
ENSE00002477386	62413732	62413854
ENSE00003560416	62382963	62383053
ENSE00003791109	62395068	62395188

Expression profiles

Bgee: expression breadth broad, 71 present calls, max score 82.02.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.02	gold quality
testis	UBERON:0000473	65.07	gold quality
right testis	UBERON:0004534	64.32	gold quality
left testis	UBERON:0004533	63.86	gold quality
lower esophagus mucosa	UBERON:0035834	61.59	gold quality
bone marrow cell	CL:0002092	45.43	gold quality
cortical plate	UBERON:0005343	45.31	gold quality
ganglionic eminence	UBERON:0004023	45.23	gold quality
ventricular zone	UBERON:0003053	45.21	gold quality
subcutaneous adipose tissue	UBERON:0002190	44.86	gold quality
adipose tissue	UBERON:0001013	44.57	gold quality
omental fat pad	UBERON:0010414	43.94	gold quality
endometrium	UBERON:0001295	42.79	silver quality
primary visual cortex	UBERON:0002436	41.92	silver quality
esophagus mucosa	UBERON:0002469	41.73	gold quality
vermiform appendix	UBERON:0001154	41.57	silver quality
granulocyte	CL:0000094	40.95	gold quality
prefrontal cortex	UBERON:0000451	40.95	gold quality
mucosa of transverse colon	UBERON:0004991	40.62	silver quality
bone marrow	UBERON:0002371	40.02	gold quality
thoracic mammary gland	UBERON:0005200	39.78	gold quality
stromal cell of endometrium	CL:0002255	39.39	gold quality
superior frontal gyrus	UBERON:0002661	39.28	silver quality
placenta	UBERON:0001987	39.13	silver quality
skin of abdomen	UBERON:0001416	38.58	silver quality
frontal cortex	UBERON:0001870	38.15	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	37.27	silver quality
monocyte	CL:0000576	37.25	gold quality
descending thoracic aorta	UBERON:0002345	37.22	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting EFCAB3, 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-548N	99.98	71.94	4170
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-1244	99.33	68.38	832
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-558	97.50	67.16	977

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
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), CABP5 (ENSG00000105507), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CETN3 (ENSG00000153140), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CABP2 (ENSG00000167791), CALML6 (ENSG00000169885), EFCAB12 (ENSG00000172771), 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 3 — Q8N7B9 (reviewed: Q8N7B9)

All UniProt accessions (3): E5RHB1, E5RJB7, Q8N7B9

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N7B9-1	1	yes
Q8N7B9-2	2

RefSeq proteins (2): NP_001138405, NP_775774* (*=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

Pfam: PF13833

UniProt features (16 total): binding site 5, sequence variant 3, domain 2, compositionally biased region 2, chain 1, modified residue 1, splice variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7B9-F1	65.80	0.15

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 (5): 107; 96; 98; 100; 102

Post-translational modifications (1): 279

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 38 (showing top): FOXO4_01, WTGAAAT_UNKNOWN, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, LEIN_MEDULLA_MARKERS, chr17q23, FOXO3_01, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, MIR451B, WP_CLEAR_CELL_RENAL_CELL_CARCINOMA_PATHWAYS, DESCARTES_MAIN_FETAL_PDE1C_ACSM3_POSITIVE_CELLS, GSE17974_0H_VS_48H_IN_VITRO_ACT_CD4_TCELL_DN, GSE17974_0H_VS_72H_IN_VITRO_ACT_CD4_TCELL_DN, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_0.5H_ACT_CD4_TCELL_DN, NF1_Q6, GSE37416_CTRL_VS_3H_F_TULARENSIS_LVS_NEUTROPHIL_DN

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:

Category	Terms
metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

1895 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EFCAB3	IQCF2	Q8IXL9	674
EFCAB3	METTL2A	Q96IZ6	638
EFCAB3	SMLR1	H3BR10	599
EFCAB3	METTL2B	Q6P1Q9	584
EFCAB3	MARCHF10	Q8NA82	570
EFCAB3	KANSL1	Q7Z3B3	460
EFCAB3	CEP41	Q9BYV8	459
EFCAB3	SYTL1	Q8IYJ3	457
EFCAB3	MAGEE2	Q8TD90	451
EFCAB3	KIAA1210	Q9ULL0	445
EFCAB3	TLK2	Q86UE8	440
EFCAB3	CRHR1	P34998	404
EFCAB3	EFCAB13	Q8IY85	395
EFCAB3	HPCAL1	P37235	394
EFCAB3	BCAS3	Q9H6U6	390

IntAct

1 interactions, top by confidence:

BioGRID (19): EFCAB3 (Affinity Capture-MS), EFCAB3 (Two-hybrid), EFCAB3 (Two-hybrid), EFCAB3 (Two-hybrid), EFCAB3 (Two-hybrid), EFCAB3 (Two-hybrid), EFCAB3 (Two-hybrid), SPERT (Two-hybrid), KRT35 (Two-hybrid), WWP2 (Two-hybrid), EFCAB3 (Proximity Label-MS), EFCAB3 (Proximity Label-MS), EFCAB3 (Proximity Label-MS), EFCAB3 (Proximity Label-MS), EFCAB3 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GVH7, A6PVS8, A8DZJ1, A9Q751, D3ZSP7, D4AEC2, Q08AD1, Q08CX2, Q14DL3, Q2T9P0, Q2TA00, Q32KQ1, Q3UZ57, Q3V0J4, Q4G0U5, Q4R7B1, Q4R7Z7, Q5S003, Q5SUV2, Q5T1B0, Q5ZLS8, Q63164, Q66HC0, Q69CM7, Q6AXP3, Q6AYL8, Q6IRN6, Q6NXP0, Q6Q759, Q80X60, Q86WZ0, Q8C1B1, Q8C4J0, Q8C636, Q8CDN1, Q8CDU5, Q8IWF9, Q8N7B9, Q8N7U6, Q8ND61

Diamond homologs: O74435, P02597, P04464, P05419, P13868, P15845, P25071, P27161, P27163, Q0IQB6, Q0IUU4, Q2T9P0, Q40302, Q41420, Q4R736, Q66HC0, Q68A65, Q7Z572, Q80X60, Q84MN0, Q8BHW6, Q8K4K1, Q8N7B9, Q9LE22, A3E3H0, A3E4D8, A3E4F9, A4UHC0, A8I1Q0, O02367, O16305, O82018, O82659, O96081, O97341, P02591, P02598, P02599, P04352, P07463

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	43
Likely benign	3
Benign	4

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
153259	GRCh38/hg38 17q23.2(chr17:62039036-62927189)x3	Likely pathogenic

SpliceAI

1514 predictions. Top by Δscore:

Variant	Effect	Δscore
17:62391817:CCCA:C	acceptor_loss	1.0000
17:62391819:CA:C	acceptor_loss	1.0000
17:62391820:A:AG	acceptor_gain	1.0000
17:62391820:A:G	acceptor_loss	1.0000
17:62391821:G:GG	acceptor_gain	1.0000
17:62391821:GCT:G	acceptor_gain	1.0000
17:62391962:GATC:G	donor_gain	1.0000
17:62391964:TC:T	donor_gain	1.0000
17:62391966:G:GG	donor_gain	1.0000
17:62406672:GA:G	donor_gain	1.0000
17:62406674:G:GG	donor_gain	1.0000
17:62387395:C:G	donor_gain	0.9900
17:62391821:GC:G	acceptor_gain	0.9900
17:62391821:GCTTT:G	acceptor_gain	0.9900
17:62391961:TGATC:T	donor_gain	0.9900
17:62391962:GATCG:G	donor_gain	0.9900
17:62391963:ATC:A	donor_gain	0.9900
17:62391965:CGTG:C	donor_loss	0.9900
17:62391966:G:T	donor_loss	0.9900
17:62391967:T:TG	donor_loss	0.9900
17:62391968:G:GC	donor_loss	0.9900
17:62391969:A:AC	donor_loss	0.9900
17:62391970:G:C	donor_loss	0.9900
17:62395065:T:G	acceptor_gain	0.9900
17:62395066:A:AG	acceptor_gain	0.9900
17:62395067:G:GA	acceptor_gain	0.9900
17:62395184:GTAAG:G	donor_gain	0.9900
17:62395185:TAAGG:T	donor_loss	0.9900
17:62395186:AAG:A	donor_loss	0.9900
17:62395189:GTAA:G	donor_loss	0.9900

AlphaMissense

2904 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:62416072:T:A	W354R	0.981
17:62416072:T:C	W354R	0.981
17:62416150:T:A	W380R	0.979
17:62416150:T:C	W380R	0.979
17:62416156:T:A	W382R	0.976
17:62416156:T:C	W382R	0.976
17:62391825:T:C	F52S	0.974
17:62393599:T:C	F108L	0.974
17:62393601:T:A	F108L	0.974
17:62393601:T:G	F108L	0.974
17:62416135:T:C	F375L	0.973
17:62416137:T:A	F375L	0.973
17:62416137:T:G	F375L	0.973
17:62416074:G:C	W354C	0.972
17:62416074:G:T	W354C	0.972
17:62393600:T:C	F108S	0.968
17:62416136:T:C	F375S	0.964
17:62416158:G:C	W382C	0.963
17:62416158:G:T	W382C	0.963
17:62406604:T:C	F205L	0.962
17:62406606:T:A	F205L	0.962
17:62406606:T:G	F205L	0.962
17:62416123:T:C	F371L	0.962
17:62416125:T:A	F371L	0.962
17:62416125:T:G	F371L	0.962
17:62391824:T:C	F52L	0.960
17:62391826:C:A	F52L	0.960
17:62391826:C:G	F52L	0.960
17:62416152:G:C	W380C	0.959
17:62416152:G:T	W380C	0.959

dbSNP variants (sampled 300 via entrez): RS1000038665 (17:62376025 C>A), RS1000156402 (17:62375995 A>C), RS1000211216 (17:62369768 T>C), RS1000259929 (17:62389218 C>G), RS1000305907 (17:62370091 A>G), RS1000347926 (17:62395367 C>T), RS1000348470 (17:62407462 T>C), RS1000420516 (17:62407754 C>A,T), RS1000423642 (17:62375741 A>T), RS1000500627 (17:62376369 C>A), RS1000580829 (17:62400612 T>C), RS1000647739 (17:62402248 G>A), RS1000651707 (17:62393638 G>A,T), RS1000654961 (17:62371372 T>C,G), RS1000679877 (17:62409144 A>T)

Disease associations

OMIM: gene MIM:619567 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003159_4	Objective response to lithium treatment	4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	decreases methylation, increases methylation	2
graphene oxide	increases expression	1
trichostatin A	affects expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
CGP 52608	affects binding, increases reaction	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
Benzo(a)pyrene	increases methylation	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Methyl Methanesulfonate	decreases expression	1
Nickel	decreases expression	1
Triiodothyronine	decreases expression	1

Clinical trials (associated diseases)

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