EFCAB5

Summary

EFCAB5 (EF-hand calcium binding domain 5, HGNC:24801) is a protein-coding gene on chromosome 17q11.2, encoding EF-hand calcium-binding domain-containing protein 5 (A4FU69).

Predicted to enable calcium ion binding activity.

Source: NCBI Gene 374786 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 242 total
• MANE Select transcript: NM_198529

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24801
Approved symbol	EFCAB5
Name	EF-hand calcium binding domain 5
Location	17q11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ46247
Ensembl gene	ENSG00000176927
Ensembl biotype	protein_coding
Entrez	374786

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 6 protein_coding, 4 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000394835, ENST00000419434, ENST00000421238, ENST00000423598, ENST00000440741, ENST00000448319, ENST00000534836, ENST00000536908, ENST00000581617, ENST00000582953, ENST00000584826, ENST00000588978, ENST00000638539

RefSeq mRNA: 2 — MANE Select: NM_198529 NM_001145053, NM_198529

CCDS: CCDS11254, CCDS54103

Canonical transcript exons

ENST00000394835 — 23 exons

Exon	Start	End
ENSE00001261282	30092840	30092936
ENSE00001261289	30091871	30092157
ENSE00001261302	30090421	30090674
ENSE00001372353	30082891	30083043
ENSE00001375523	30078215	30078504
ENSE00001380005	30080753	30080981
ENSE00001384378	30080072	30080241
ENSE00001388001	30087063	30087166
ENSE00001478572	30059545	30059701
ENSE00001623625	29968791	29969367
ENSE00001731150	29941634	29941838
ENSE00001743278	30107834	30108452
ENSE00003469772	30034230	30034385
ENSE00003470995	29999906	29999976
ENSE00003472043	30051118	30051217
ENSE00003479446	30055888	30055965
ENSE00003497859	30057676	30057890
ENSE00003507326	29943565	29943649
ENSE00003516306	30053255	30054148
ENSE00003543726	29996312	29996360
ENSE00003584771	29993165	29993321
ENSE00003590965	30056064	30056156
ENSE00003591261	29942240	29942302

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 82.21.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5335 / max 28.7072, expressed in 283 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160119	0.5274	281
160120	0.0061	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	82.21	gold quality
sperm	CL:0000019	82.15	gold quality
right testis	UBERON:0004534	80.86	gold quality
testis	UBERON:0000473	80.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.21	gold quality
buccal mucosa cell	CL:0002336	75.95	gold quality
sural nerve	UBERON:0015488	71.15	gold quality
ganglionic eminence	UBERON:0004023	68.65	gold quality
monocyte	CL:0000576	68.63	gold quality
mucosa of paranasal sinus	UBERON:0005030	68.55	gold quality
leukocyte	CL:0000738	67.91	gold quality
mucosa of transverse colon	UBERON:0004991	67.73	gold quality
cortical plate	UBERON:0005343	67.49	gold quality
rectum	UBERON:0001052	67.39	gold quality
stromal cell of endometrium	CL:0002255	66.88	gold quality
cerebellar hemisphere	UBERON:0002245	64.45	gold quality
cerebellar cortex	UBERON:0002129	64.36	gold quality
adrenal tissue	UBERON:0018303	63.17	gold quality
colonic epithelium	UBERON:0000397	62.90	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.80	gold quality
cerebellum	UBERON:0002037	62.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	62.74	gold quality
transverse colon	UBERON:0001157	62.59	gold quality
metanephros cortex	UBERON:0010533	62.30	gold quality
islet of Langerhans	UBERON:0000006	62.16	gold quality
corpus callosum	UBERON:0002336	61.63	gold quality
prefrontal cortex	UBERON:0000451	61.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	61.02	gold quality
anterior cingulate cortex	UBERON:0009835	60.87	gold quality
epithelium of nasopharynx	UBERON:0001951	60.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting EFCAB5, 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-4795-3P	100.00	74.62	4024
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-4524A-5P	99.57	71.73	1193
HSA-MIR-4524B-5P	99.57	71.68	1195
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-922	99.02	67.23	1838

Literature-anchored findings (GeneRIF, showing 1)

• EFCAB5 gene expression is decreased in papillary thyroid carcinoma. (PMID:21509594)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Efcab5	ENSMUSG00000050944
rattus_norvegicus	Efcab5	ENSRNOG00000022536
drosophila_melanogaster	CG15747	FBGN0030474
caenorhabditis_elegans		WBGENE00007627

Paralogs (1): NSRP1 (ENSG00000126653)

Protein

Protein identifiers

EF-hand calcium-binding domain-containing protein 5 — A4FU69 (reviewed: A4FU69)

All UniProt accessions (5): A4FU69, C9J1E6, H0Y4M1, H0Y843, K7EJC3

UniProt curated annotations — full annotation on UniProt →

Isoforms (6)

UniProt ID	Names	Canonical?
A4FU69-1	1	yes
A4FU69-2	2
A4FU69-3	3
A4FU69-4	4
A4FU69-5	5
A4FU69-6	6

RefSeq proteins (2): NP_001138525, NP_940931* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR029016	GAF-like_dom_sf	Homologous_superfamily

UniProt features (34 total): splice variant 8, sequence variant 6, sequence conflict 5, binding site 4, region of interest 4, compositionally biased region 4, chain 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4FU69-F1	68.22	0.19

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 (4): 882; 884; 886; 893

Post-translational modifications (1): 77

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 57 (showing top): chr17q11, LYF1_01, CCCNNGGGAR_OLF1_01, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, ATF6_TARGET_GENES, BARX1_TARGET_GENES, GLI3_TARGET_GENES, HES4_TARGET_GENES, HOXC13_TARGET_GENES, HOXD11_TARGET_GENES, LHX9_TARGET_GENES, NR1I2_TARGET_GENES, ZIM3_TARGET_GENES, MIR153_5P, MIR607

GO Biological Process (0):

GO Molecular Function (2): calcium ion binding (GO:0005509), 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
cation binding	1

Protein interactions and networks

STRING

724 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EFCAB5	NSRP1	Q9H0G5	552
EFCAB5	A0A0J9YXS1	A0A0J9YXS1	540
EFCAB5	CCDC116	Q8IYX3	507
EFCAB5	TOR2A	Q5JU69	457
EFCAB5	PEX39	Q5I0X4	447
EFCAB5	KPNA4	O00629	415
EFCAB5	ERICH6	Q7L0X2	413
EFCAB5	SMC4	Q9NTJ3	412
EFCAB5	RIPOR3	Q96MK2	410
EFCAB5	TCF23	Q7RTU1	410
EFCAB5	CRLF3	Q8IUI8	396
EFCAB5	ZMAT4	Q9H898	389
EFCAB5	TEKTL1	Q8IYK2	384
EFCAB5	TRAPPC13	A5PLN9	383
EFCAB5	AADACL3	Q5VUY0	377

IntAct

6 interactions, top by confidence:

A	B	Type	Score
EFCAB5	H1-5	psi-mi:“MI:0915”(physical association)	0.400
EFCAB5	iglC2	psi-mi:“MI:0915”(physical association)	0.370
	ESYT2	psi-mi:“MI:0914”(association)	0.350
CTNNA1	EFCAB5	psi-mi:“MI:0914”(association)	0.350
GATA2	EFCAB5	psi-mi:“MI:0914”(association)	0.350

BioGRID (19): EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Synthetic Lethality), HIST1H1B (Proximity Label-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Reconstituted Complex), LMNA (Cross-Linking-MS (XL-MS)), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS), EFCAB5 (Affinity Capture-MS)

ESM2 similar proteins: A0JP43, A2AHC3, A2RRS8, A2VCV0, A4FU69, A4IG55, A5WUN7, A8T6P4, D3Z6S9, D3Z8E6, D4AEC2, E7F7X0, F7EC58, G3UZ78, Q06190, Q08AD1, Q2MJV9, Q3KQW7, Q3UH68, Q3UMB5, Q3V036, Q5SUV2, Q5T5Y3, Q5ZM60, Q640L3, Q640U0, Q66H73, Q69CM7, Q6AYC8, Q6IRN6, Q6PG04, Q6Q759, Q76LL6, Q76N89, Q7L0X2, Q80VH0, Q8C1B1, Q8C627, Q8CCG4, Q8CDN1

Diamond homologs: A0JP43, A4FU69

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	180
Likely benign	40
Benign	10

Top pathogenic / likely-pathogenic (0)

SpliceAI

4282 predictions. Top by Δscore:

Variant	Effect	Δscore
17:29943561:A:AG	acceptor_gain	1.0000
17:29943562:A:AG	acceptor_gain	1.0000
17:29943563:A:G	acceptor_gain	1.0000
17:29943564:G:GA	acceptor_gain	1.0000
17:29943564:G:GC	acceptor_loss	1.0000
17:29943564:GA:G	acceptor_gain	1.0000
17:29943564:GAC:G	acceptor_gain	1.0000
17:29943645:CCAAG:C	donor_loss	1.0000
17:29943646:CAAG:C	donor_loss	1.0000
17:29943647:AAG:A	donor_loss	1.0000
17:29943648:AGGTA:A	donor_loss	1.0000
17:29943649:GGT:G	donor_loss	1.0000
17:29943650:G:C	donor_loss	1.0000
17:29943651:T:A	donor_loss	1.0000
17:29968789:A:AG	acceptor_gain	1.0000
17:29968790:G:GG	acceptor_gain	1.0000
17:29996356:GCTTG:G	donor_gain	1.0000
17:29996361:GT:G	donor_loss	1.0000
17:29996363:AA:A	donor_loss	1.0000
17:29999899:T:G	acceptor_gain	1.0000
17:29999901:A:G	acceptor_gain	1.0000
17:29999974:G:GT	donor_gain	1.0000
17:29999974:GAA:G	donor_gain	1.0000
17:29999977:G:GG	donor_gain	1.0000
17:30034228:A:AG	acceptor_gain	1.0000
17:30034229:G:GG	acceptor_gain	1.0000
17:30034229:GT:G	acceptor_gain	1.0000
17:30034229:GTA:G	acceptor_gain	1.0000
17:30034229:GTAC:G	acceptor_gain	1.0000
17:30034382:GAAGG:G	donor_loss	1.0000

AlphaMissense

9980 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:29993283:T:A	W296R	0.995
17:29993283:T:C	W296R	0.995
17:30080240:A:C	S1066R	0.994
17:30080753:C:A	S1066R	0.994
17:30080753:C:G	S1066R	0.994
17:30080788:T:A	V1078D	0.990
17:30080859:T:C	S1102P	0.989
17:30080106:C:A	A1021D	0.988
17:30080866:T:C	L1104P	0.988
17:30078497:T:C	L1007P	0.987
17:30051217:T:A	W434R	0.986
17:30051217:T:C	W434R	0.986
17:30080095:A:C	K1017N	0.986
17:30080095:A:T	K1017N	0.986
17:30080953:T:C	F1133S	0.986
17:29993251:G:C	R285P	0.985
17:30080075:G:C	A1011P	0.985
17:30080754:T:C	F1067L	0.985
17:30080756:T:A	F1067L	0.985
17:30080756:T:G	F1067L	0.985
17:30080973:T:C	F1140L	0.985
17:30080975:C:A	F1140L	0.985
17:30080975:C:G	F1140L	0.985
17:30080072:G:C	D1010H	0.984
17:30080102:A:C	S1020R	0.984
17:30080104:T:A	S1020R	0.984
17:30080104:T:G	S1020R	0.984
17:30080857:G:A	G1101D	0.984
17:29993285:G:C	W296C	0.982
17:29993285:G:T	W296C	0.982

dbSNP variants (sampled 300 via entrez): RS1000001681 (17:29932190 A>C), RS1000008821 (17:30097669 G>T), RS1000024923 (17:29930338 G>T), RS1000064949 (17:30030587 C>T), RS1000068039 (17:30083643 G>A,C), RS1000122080 (17:29999294 A>G), RS1000133065 (17:29951418 A>C), RS1000136851 (17:30090758 T>C), RS1000166561 (17:30061216 C>G,T), RS1000171145 (17:30021037 A>G), RS1000173688 (17:29971966 T>C), RS1000176614 (17:30028918 A>G), RS1000206185 (17:29972249 C>T), RS1000211394 (17:30070703 A>T), RS1000217409 (17:29961102 A>G)

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

12 associations (top):

Study	Trait	p-value
GCST002650_7	Coffee consumption (cups per day)	3.000000e-08
GCST003872_16	QRS complex (12-leadsum)	6.000000e-09
GCST004185_19	Lung function (FEV1/FVC)	7.000000e-18
GCST007692_1	Chronic obstructive pulmonary disease	1.000000e-08
GCST010083_157	Hemoglobin levels	3.000000e-08
GCST010083_215	Hemoglobin levels	1.000000e-10
GCST010320_8	PR interval	3.000000e-11
GCST010321_40	PR interval	3.000000e-11
GCST010703_115	Brain morphology (MOSTest)	1.000000e-28
GCST010796_5176	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-09
GCST010796_5177	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST011766_34	Chronic obstructive pulmonary disease	2.000000e-07

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004330	coffee consumption
EFO:0006782	cups of coffee per day measurement
EFO:0005054	QRS complex
EFO:0007742	QRS amplitude
EFO:0004713	FEV/FVC ratio
EFO:0004509	hemoglobin measurement
EFO:0004462	PR interval
EFO:0004346	neuroimaging measurement
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
bisphenol A	affects cotreatment, affects methylation	1
sodium arsenite	decreases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Amiodarone	increases expression	1
Arsenic	affects methylation	1
N-Nitrosopyrrolidine	decreases expression	1

Clinical trials (associated diseases)

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