EFCAB11

Summary

EFCAB11 (EF-hand calcium binding domain 11, HGNC:20357) is a protein-coding gene on chromosome 14q32.11, encoding EF-hand calcium-binding domain-containing protein 11 (Q9BUY7).

Predicted to enable calcium ion binding activity and enzyme regulator activity. Predicted to be involved in microtubule cytoskeleton organization. Predicted to be active in cytoplasm.

Source: NCBI Gene 90141 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_145231

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20357
Approved symbol	EFCAB11
Name	EF-hand calcium binding domain 11
Location	14q32.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000140025
Ensembl biotype	protein_coding
Entrez	90141

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 7 protein_coding, 5 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000316738, ENST00000538485, ENST00000550103, ENST00000553871, ENST00000554761, ENST00000555430, ENST00000555608, ENST00000555872, ENST00000556005, ENST00000556078, ENST00000556609, ENST00000556639, ENST00000557685, ENST00000905285, ENST00000905286

RefSeq mRNA: 5 — MANE Select: NM_145231 NM_001284266, NM_001284267, NM_001284268, NM_001284269, NM_145231

CCDS: CCDS61522, CCDS61523, CCDS61524, CCDS61525, CCDS9887

Canonical transcript exons

ENST00000316738 — 6 exons

Exon	Start	End
ENSE00002488705	89794669	89797324
ENSE00002499204	89954586	89954730
ENSE00003511244	89953906	89954001
ENSE00003561054	89931541	89931631
ENSE00003591472	89932526	89932627
ENSE00003593543	89950097	89950142

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 98.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0961 / max 117.1167, expressed in 1685 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
144453	5.5451	1645
144452	0.5434	305
144451	0.0076	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.93	gold quality
male germ cell	CL:0000015	97.39	gold quality
left testis	UBERON:0004533	94.35	gold quality
right testis	UBERON:0004534	94.08	gold quality
testis	UBERON:0000473	92.52	gold quality
oocyte	CL:0000023	90.16	gold quality
secondary oocyte	CL:0000655	89.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.07	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	84.84	gold quality
adult organism	UBERON:0007023	84.57	gold quality
bronchial epithelial cell	CL:0002328	84.56	gold quality
epithelium of bronchus	UBERON:0002031	84.12	gold quality
calcaneal tendon	UBERON:0003701	83.43	gold quality
bronchus	UBERON:0002185	83.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.56	gold quality
ventricular zone	UBERON:0003053	81.86	gold quality
pancreatic ductal cell	CL:0002079	81.55	silver quality
epithelium of nasopharynx	UBERON:0001951	80.30	gold quality
esophagus squamous epithelium	UBERON:0006920	80.10	gold quality
adrenal tissue	UBERON:0018303	79.92	gold quality
epithelium of esophagus	UBERON:0001976	79.08	gold quality
rectum	UBERON:0001052	78.82	gold quality
islet of Langerhans	UBERON:0000006	78.79	gold quality
endometrium	UBERON:0001295	78.57	gold quality
nasal cavity epithelium	UBERON:0005384	78.55	gold quality
nasal cavity mucosa	UBERON:0001826	78.46	gold quality
gingival epithelium	UBERON:0001949	78.45	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.11	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.04	gold quality
embryo	UBERON:0000922	77.80	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

61 targeting EFCAB11, 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-6867-5P	100.00	82.21	3464
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-3913-3P	99.74	66.53	938
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-567	99.63	68.57	1219
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-3616-5P	99.55	67.02	989

Literature-anchored findings (GeneRIF, showing 1)

• This work reported the association of 14q32.11 (EFCAB11) with Hepatocellular carcinoma in Chinese Han population and revealed the genetic interaction between STAT4 (2q32.2-q32.3) and EFCAB11 (14q32.11) in Hepatocellular carcinoma. (PMID:25665738)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	efcab11	ENSDARG00000043740
mus_musculus	Efcab11	ENSMUSG00000021176
rattus_norvegicus	Efcab11	ENSRNOG00000053317

Protein

Protein identifiers

EF-hand calcium-binding domain-containing protein 11 — Q9BUY7 (reviewed: Q9BUY7)

All UniProt accessions (2): Q9BUY7, H0YJX4

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (6)

UniProt ID	Names	Canonical?
Q9BUY7-1	1	yes
Q9BUY7-2	2
Q9BUY7-3	3
Q9BUY7-4	4
Q9BUY7-5	5
Q9BUY7-6	6

RefSeq proteins (5): NP_001271195, NP_001271196, NP_001271197, NP_001271198, NP_660274* (*=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
IPR050403	Myosin_RLC	Family

Pfam: PF13499, PF13833

UniProt features (18 total): splice variant 6, binding site 5, domain 3, sequence variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BUY7-F1	87.38	0.71

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): 140; 142; 144; 146; 151

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, AACTTT_UNKNOWN, chr14q32, NUYTTEN_EZH2_TARGETS_DN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOMF_ENZYME_REGULATOR_ACTIVITY, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN, GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION, FORTSCHEGGER_PHF8_TARGETS_DN, LTE2_UP.V1_UP, TAVAZOIE_METASTASIS, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP

GO Biological Process (1): microtubule cytoskeleton organization (GO:0000226)

GO Molecular Function (4): calcium ion binding (GO:0005509), enzyme regulator activity (GO:0030234), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoskeleton organization	1
microtubule-based process	1
metal ion binding	1
catalytic activity	1
molecular function regulator activity	1
binding	1
cation binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1757 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EFCAB11	IQCK	Q8N0W5	651
EFCAB11	MCTP1	Q6DN14	618
EFCAB11	DPY19L1	Q2PZI1	589
EFCAB11	MAP4K3	Q8IVH8	511
EFCAB11	EFCC1	Q9HA90	508
EFCAB11	FAM117B	Q6P1L5	504
EFCAB11	DRC8	Q5VUJ9	497
EFCAB11	DTNA	Q9Y4J8	493
EFCAB11	EFCAB7	A8K855	481
EFCAB11	RBM43	Q6ZSC3	440
EFCAB11	TDP1	Q9NUW8	435
EFCAB11	EFHC2	Q5JST6	426
EFCAB11	CLXN	Q9HAE3	404
EFCAB11	CFAP263	Q9H0I3	391
EFCAB11	CFAP20	Q9Y6A4	391

IntAct

16 interactions, top by confidence:

A	B	Type	Score
CETN1	SFI1	psi-mi:“MI:0914”(association)	0.640
EFCAB11	MSRA	psi-mi:“MI:0915”(physical association)	0.560
AKR1B1	EFCAB11	psi-mi:“MI:0915”(physical association)	0.560
EFCAB11	SFI1	psi-mi:“MI:0914”(association)	0.530
EFCAB11	CFTR	psi-mi:“MI:0915”(physical association)	0.370
CFTR	EFCAB11	psi-mi:“MI:0915”(physical association)	0.370
EFCAB11	MSRA	psi-mi:“MI:0915”(physical association)	0.000
AKR1B1	EFCAB11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): EFCAB11 (Affinity Capture-RNA), EFCAB11 (Affinity Capture-RNA), EFCAB11 (Affinity Capture-MS), EFCAB11 (Two-hybrid), MSRA (Two-hybrid), CETN2 (Affinity Capture-MS), UBB (Affinity Capture-MS), DLG1 (Affinity Capture-MS), SFI1 (Affinity Capture-MS), BLK (Affinity Capture-MS), EFCAB11 (Affinity Capture-MS), CASK (Affinity Capture-MS), MPP7 (Affinity Capture-MS), CETN3 (Affinity Capture-MS), UBR3 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I6A2H6, A2A2Y4, F1LQY6, O43379, O94806, O95267, P0C0T1, Q13572, Q17QD9, Q2KI69, Q32L26, Q3LAC4, Q3U3T8, Q3UGM2, Q496Y0, Q5R803, Q5RHX6, Q69ZK0, Q6PHZ8, Q6PIL6, Q70Z35, Q86XE3, Q8BWW9, Q8BYN3, Q8CCA0, Q8HXL3, Q8HYN7, Q8K1Y2, Q8R426, Q8TCU6, Q8WN03, Q91ZP9, Q92564, Q96GE6, Q99MG9, Q9BUY7, Q9CTY5, Q9D3N2, Q9HAE3, Q9HBU6

Diamond homologs: Q568G4, Q6AXQ2, Q9BUY7, Q9D0E5, Q9SRP4, Q619T5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2008 predictions. Top by Δscore:

Variant	Effect	Δscore
14:89931536:CTTAC:C	donor_loss	1.0000
14:89931537:TTA:T	donor_loss	1.0000
14:89931538:TACCT:T	donor_loss	1.0000
14:89931539:ACCT:A	donor_loss	1.0000
14:89931540:CC:C	donor_loss	1.0000
14:89931628:CGAT:C	acceptor_gain	1.0000
14:89931629:GATCT:G	acceptor_loss	1.0000
14:89931630:ATC:A	acceptor_loss	1.0000
14:89931631:TC:T	acceptor_loss	1.0000
14:89931632:C:A	acceptor_loss	1.0000
14:89931632:C:CC	acceptor_gain	1.0000
14:89931636:T:C	acceptor_gain	1.0000
14:89931636:T:TC	acceptor_gain	1.0000
14:89932521:CTTA:C	donor_loss	1.0000
14:89932522:TTA:T	donor_loss	1.0000
14:89932523:TAC:T	donor_loss	1.0000
14:89932524:A:AC	donor_gain	1.0000
14:89932524:A:C	donor_loss	1.0000
14:89932525:C:CT	donor_gain	1.0000
14:89932525:CA:C	donor_gain	1.0000
14:89932525:CAG:C	donor_gain	1.0000
14:89932525:CAGT:C	donor_gain	1.0000
14:89932525:CAGTA:C	donor_gain	1.0000
14:89932623:TATAC:T	acceptor_gain	1.0000
14:89932624:ATAC:A	acceptor_gain	1.0000
14:89932625:TAC:T	acceptor_gain	1.0000
14:89932628:C:CA	acceptor_loss	1.0000
14:89932628:C:CC	acceptor_gain	1.0000
14:89932629:T:G	acceptor_loss	1.0000
14:89932635:T:C	acceptor_gain	1.0000

AlphaMissense

1075 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:89797295:A:T	V147D	0.994
14:89932545:G:C	F100L	0.994
14:89932545:G:T	F100L	0.994
14:89932547:A:G	F100L	0.994
14:89931621:A:C	F110L	0.993
14:89931621:A:T	F110L	0.993
14:89931623:A:G	F110L	0.993
14:89931619:A:G	L111S	0.989
14:89953940:G:T	A46D	0.989
14:89953941:C:G	A46P	0.989
14:89931543:G:C	F136L	0.987
14:89931543:G:T	F136L	0.987
14:89931545:A:G	F136L	0.987
14:89932546:A:G	F100S	0.986
14:89797291:G:C	S148R	0.984
14:89797291:G:T	S148R	0.984
14:89797293:T:G	S148R	0.984
14:89932533:G:C	D104E	0.984
14:89932533:G:T	D104E	0.984
14:89932609:A:G	F79S	0.983
14:89953945:T:A	K44N	0.983
14:89953945:T:G	K44N	0.983
14:89953964:A:T	L38H	0.982
14:89953996:A:C	F27L	0.982
14:89953996:A:T	F27L	0.982
14:89953998:A:G	F27L	0.982
14:89932535:C:G	D104H	0.981
14:89932534:T:G	D104A	0.979
14:89931625:C:T	G109E	0.978
14:89932608:A:C	F79L	0.978

dbSNP variants (sampled 300 via entrez): RS1000046112 (14:89916164 A>G), RS1000052067 (14:89809059 G>C), RS1000074827 (14:89835677 G>A,C), RS1000078327 (14:89846540 G>A,T), RS1000106371 (14:89818441 C>T), RS1000144713 (14:89871033 C>T), RS1000146350 (14:89909923 C>G), RS1000157807 (14:89862971 G>A), RS1000228703 (14:89876498 T>C), RS1000232906 (14:89945691 T>C), RS1000239101 (14:89845856 G>A), RS1000250988 (14:89945348 T>C), RS1000305447 (14:89938795 C>G,T), RS1000309457 (14:89855562 T>C), RS1000363259 (14:89896641 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000902_1	Hepatocellular carcinoma	4.000000e-06
GCST001823_20	Metabolite levels (HVA/MHPG ratio)	2.000000e-06
GCST001859_54	Thiazide-induced adverse metabolic effects in hypertensive patients	6.000000e-06
GCST009391_836	Metabolite levels	7.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005131	HVA measurement
EFO:0005133	MHPG measurement
EFO:0004530	triglyceride measurement
EFO:0010399	triacylglycerol 44:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression	4
Cyclosporine	decreases expression	3
bisphenol A	decreases methylation, increases methylation, affects expression, affects cotreatment	2
Aflatoxin B1	affects expression, decreases expression, decreases methylation	2
dicrotophos	decreases expression	1
methyleugenol	decreases expression	1
propionaldehyde	decreases expression	1
sodium arsenite	increases expression, affects cotreatment, increases abundance	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
pentanal	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Azathioprine	decreases expression	1
Cadmium	increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Quercetin	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	increases expression, increases abundance	1
Tetrachlorodibenzodioxin	increases expression	1

Clinical trials (associated diseases)

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