EFCC1

Summary

EFCC1 (EF-hand and coiled-coil domain containing 1, HGNC:25692) is a protein-coding gene on chromosome 3q21.3, encoding EF-hand and coiled-coil domain-containing protein 1 (Q9HA90).

Predicted to enable calcium ion binding activity.

Source: NCBI Gene 79825 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_001377500

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25692
Approved symbol	EFCC1
Name	EF-hand and coiled-coil domain containing 1
Location	3q21.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12057
Ensembl gene	ENSG00000114654
Ensembl biotype	protein_coding
Entrez	79825

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000436022, ENST00000481536, ENST00000683648, ENST00000947983

RefSeq mRNA: 2 — MANE Select: NM_001377500 NM_001377500, NM_024768

CCDS: CCDS3054, CCDS93371

Canonical transcript exons

ENST00000683648 — 8 exons

Exon	Start	End
ENSE00002283176	129039712	129040742
ENSE00003487213	129030703	129030860
ENSE00003495284	129036977	129037117
ENSE00003514126	129038831	129038900
ENSE00003522103	129003794	129004077
ENSE00003616422	129034164	129034329
ENSE00003917437	129001304	129002324
ENSE00003918329	129032819	129032966

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 82.92.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7301 / max 45.8352, expressed in 291 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38496	0.3549	180
38497	0.2318	124
38495	0.1434	91

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper lobe of left lung	UBERON:0008952	82.92	gold quality
right lung	UBERON:0002167	81.58	gold quality
upper lobe of lung	UBERON:0008948	81.21	gold quality
type B pancreatic cell	CL:0000169	81.14	gold quality
olfactory bulb	UBERON:0002264	80.91	gold quality
apex of heart	UBERON:0002098	80.34	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.62	gold quality
left ovary	UBERON:0002119	77.54	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.15	gold quality
right ovary	UBERON:0002118	77.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.00	gold quality
lower esophagus	UBERON:0013473	76.94	gold quality
gall bladder	UBERON:0002110	76.55	gold quality
spleen	UBERON:0002106	76.11	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.04	gold quality
mucosa of transverse colon	UBERON:0004991	75.95	gold quality
lung	UBERON:0002048	75.49	gold quality
small intestine Peyer’s patch	UBERON:0003454	75.09	gold quality
body of stomach	UBERON:0001161	74.42	gold quality
transverse colon	UBERON:0001157	74.40	gold quality
small intestine	UBERON:0002108	73.95	gold quality
tongue squamous epithelium	UBERON:0006919	73.49	gold quality
left lobe of thyroid gland	UBERON:0001120	73.42	gold quality
right lobe of thyroid gland	UBERON:0001119	73.31	gold quality
ovary	UBERON:0000992	72.89	gold quality
colonic epithelium	UBERON:0000397	72.82	gold quality
fundus of stomach	UBERON:0001160	72.67	gold quality
stomach	UBERON:0000945	72.64	gold quality
thyroid gland	UBERON:0002046	72.55	gold quality
mucosa of stomach	UBERON:0001199	72.42	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting EFCC1, 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-6873-3P	100.00	71.42	2626
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-1909-3P	99.03	66.56	1662

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	eef1db	ENSDARG00000030053
danio_rerio	eef1da	ENSDARG00000102291
mus_musculus	Efcc1	ENSMUSG00000068263
rattus_norvegicus	Efcc1	ENSRNOG00000009787
drosophila_melanogaster	eEF1beta	FBGN0028737
drosophila_melanogaster	eEF1delta	FBGN0032198
caenorhabditis_elegans		WBGENE00018846

Paralogs (2): EEF1D (ENSG00000104529), EEF1B2 (ENSG00000114942)

Protein

Protein identifiers

EF-hand and coiled-coil domain-containing protein 1 — Q9HA90 (reviewed: Q9HA90)

Alternative names: Coiled-coil domain-containing protein 48

All UniProt accessions (2): A0A804HK68, Q9HA90

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q9HA90-1	1	yes
Q9HA90-2	2

RefSeq proteins (2): NP_001364429, NP_079044 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR031601	CCD48	Family

Pfam: PF15799

UniProt features (13 total): region of interest 4, compositionally biased region 3, coiled-coil region 2, chain 1, domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HA90-F1	69.76	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): MODULE_255, MODULE_317, chr3q21, MODULE_95, MODULE_69, MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, MODULE_49, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, MODULE_37, GENTLES_LEUKEMIC_STEM_CELL_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MODULE_163, MIR6873_3P, MIR4700_5P

GO Biological Process (0):

GO Molecular Function (1): calcium ion binding (GO:0005509)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
metal ion binding	1

Protein interactions and networks

STRING

274 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EFCC1	D6RC18	D6RC18	600
EFCC1	ISY1	Q9ULR0	581
EFCC1	TMEM89	A2RUT3	580
EFCC1	HDHD5	Q9BXW7	571
EFCC1	PET100	P0DJ07	537
EFCC1	EFCAB11	Q9BUY7	508
EFCC1	GARIN5A	Q6IPT2	480
EFCC1	EFHC2	Q5JST6	472
EFCC1	CLXN	Q9HAE3	452
EFCC1	RAB43	Q86YS6	448
EFCC1	EFCAB7	A8K855	447
EFCC1	CALHM3	Q86XJ0	445
EFCC1	CALHM2	Q9HA72	433
EFCC1	TMEM234	Q8WY98	431
EFCC1	CHERP	Q8IWX8	429

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CUL1	LGALS8	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): EFCC1 (Affinity Capture-MS), EFCC1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

Diamond homologs: P0CG25, Q9HA90, Q9JJF6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1426 predictions. Top by Δscore:

Variant	Effect	Δscore
3:129030694:C:CA	acceptor_gain	1.0000
3:129030695:G:A	acceptor_gain	1.0000
3:129030700:CA:C	acceptor_loss	1.0000
3:129030702:GGTCA:G	acceptor_gain	1.0000
3:129030840:G:GT	donor_gain	1.0000
3:129032817:A:AG	acceptor_gain	1.0000
3:129032818:G:GG	acceptor_gain	1.0000
3:129032818:GCA:G	acceptor_gain	1.0000
3:129032818:GCAGT:G	acceptor_gain	1.0000
3:129034279:C:G	donor_gain	1.0000
3:129034284:G:GT	donor_gain	1.0000
3:129034291:GGC:G	donor_gain	1.0000
3:129034327:G:GT	donor_gain	1.0000
3:129036976:GGCA:G	acceptor_gain	1.0000
3:129037118:G:GG	donor_gain	1.0000
3:129037149:G:T	donor_gain	1.0000
3:129038828:A:AG	acceptor_gain	1.0000
3:129038829:A:G	acceptor_gain	1.0000
3:129038830:G:GG	acceptor_gain	1.0000
3:129002324:GGTGC:G	donor_loss	0.9900
3:129002325:G:A	donor_loss	0.9900
3:129002326:T:A	donor_loss	0.9900
3:129003788:CCGCA:C	acceptor_loss	0.9900
3:129003789:CGCA:C	acceptor_loss	0.9900
3:129003790:GCA:G	acceptor_loss	0.9900
3:129003791:CAGGT:C	acceptor_loss	0.9900
3:129003792:A:AC	acceptor_loss	0.9900
3:129004074:ACAGG:A	donor_loss	0.9900
3:129004076:AGGTG:A	donor_loss	0.9900
3:129004078:GTGA:G	donor_loss	0.9900

AlphaMissense

3822 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:129001713:T:A	W29R	0.999
3:129001713:T:C	W29R	0.999
3:129001715:G:C	W29C	0.999
3:129001715:G:T	W29C	0.999
3:129001795:A:T	D56V	0.999
3:129001800:T:C	Y58H	0.999
3:129001801:A:G	Y58C	0.999
3:129001815:T:C	F63L	0.999
3:129001817:C:A	F63L	0.999
3:129001817:C:G	F63L	0.999
3:129002052:T:C	F142L	0.999
3:129002054:C:A	F142L	0.999
3:129002054:C:G	F142L	0.999
3:129002062:T:C	F145S	0.999
3:129001765:A:T	N46I	0.998
3:129001766:C:A	N46K	0.998
3:129001766:C:G	N46K	0.998
3:129001768:A:T	E47V	0.998
3:129001771:T:G	I48S	0.998
3:129001804:T:C	L59P	0.998
3:129001864:T:C	F79S	0.998
3:129002061:T:C	F145L	0.998
3:129002063:C:A	F145L	0.998
3:129002063:C:G	F145L	0.998
3:129002064:C:G	H146D	0.998
3:129002149:T:C	I174T	0.998
3:129002278:T:C	L217P	0.998
3:129002302:A:T	D225V	0.998
3:129001726:C:A	A33D	0.997
3:129001771:T:A	I48N	0.997

dbSNP variants (sampled 300 via entrez): RS1000019125 (3:129002914 C>T), RS1000029659 (3:129033792 G>A), RS1000099676 (3:129032467 C>G), RS1000213318 (3:129015607 C>T), RS1000245625 (3:129026466 C>G), RS1000322764 (3:129026116 G>A,C,T), RS1000426425 (3:129032916 G>A), RS1000776860 (3:129023047 C>T), RS1000807331 (3:129040388 G>A), RS1000922066 (3:129040717 G>A), RS1000952694 (3:129015479 A>G), RS1001021142 (3:129004094 G>C,T), RS1001056530 (3:129015333 C>T), RS1001112792 (3:129016694 A>C,G), RS1001168171 (3:129034144 G>T)

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

2 associations (top):

Study	Trait	p-value
GCST90020026_221	Hip index	6.000000e-09
GCST90020028_1834	Hip circumference adjusted for BMI	4.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, decreases methylation, affects cotreatment, increases methylation	2
2,4,5,2’,4’,5’-hexachlorobiphenyl	decreases expression	1
sodium arsenite	decreases expression	1
3,4,5,3’,4’-pentachlorobiphenyl	decreases expression	1
perfluorooctanoic acid	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	decreases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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