EFCAB13

Summary

EFCAB13 (EF-hand calcium binding domain 13, HGNC:26864) is a protein-coding gene on chromosome 17q21.32, encoding EF-hand calcium-binding domain-containing protein 13 (Q8IY85).

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 173 total
• Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
• MANE Select transcript: NM_152347

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26864
Approved symbol	EFCAB13
Name	EF-hand calcium binding domain 13
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40342
Ensembl gene	ENSG00000178852
Ensembl biotype	protein_coding
Entrez	124989

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 7 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000331493, ENST00000517310, ENST00000517484, ENST00000518081, ENST00000518170, ENST00000518646, ENST00000519772, ENST00000520776, ENST00000520802, ENST00000522326, ENST00000523285, ENST00000523842, ENST00000523978

RefSeq mRNA: 6 — MANE Select: NM_152347 NM_001195192, NM_001426585, NM_001426586, NM_001426587, NM_001426588, NM_152347

CCDS: CCDS11512, CCDS56034

Canonical transcript exons

ENST00000331493 — 25 exons

Exon	Start	End
ENSE00001290173	47412773	47412916
ENSE00001293644	47404562	47404633
ENSE00001295879	47403878	47404021
ENSE00001300988	47429818	47429961
ENSE00001307770	47347808	47347951
ENSE00001312937	47414848	47414919
ENSE00001317573	47402132	47402203
ENSE00001325024	47440431	47441312
ENSE00001325117	47395834	47395977
ENSE00001327881	47409647	47409691
ENSE00001345187	47326226	47326387
ENSE00001345193	47324454	47324523
ENSE00001345198	47323955	47324074
ENSE00003463826	47374472	47374966
ENSE00003477108	47391437	47391580
ENSE00003482154	47335196	47335356
ENSE00003484763	47344162	47344292
ENSE00003515440	47377766	47377903
ENSE00003517286	47345016	47345098
ENSE00003546684	47361378	47361521
ENSE00003551650	47394025	47394099
ENSE00003558285	47379182	47379253
ENSE00003602311	47370437	47370508
ENSE00003603604	47328269	47328383
ENSE00003607642	47341921	47342032

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 92.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.5224 / max 100.8374, expressed in 1025 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161348	2.4527	1009
161347	0.0697	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	92.05	gold quality
calcaneal tendon	UBERON:0003701	91.66	gold quality
right testis	UBERON:0004534	90.97	gold quality
left testis	UBERON:0004533	90.79	gold quality
left lobe of thyroid gland	UBERON:0001120	89.89	gold quality
right lobe of thyroid gland	UBERON:0001119	89.51	gold quality
thyroid gland	UBERON:0002046	88.85	gold quality
metanephros cortex	UBERON:0010533	88.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.09	gold quality
testis	UBERON:0000473	88.00	gold quality
tendon	UBERON:0000043	84.40	gold quality
ascending aorta	UBERON:0001496	83.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.74	gold quality
thoracic aorta	UBERON:0001515	83.52	gold quality
right coronary artery	UBERON:0001625	83.49	gold quality
tibial nerve	UBERON:0001323	83.46	gold quality
right uterine tube	UBERON:0001302	83.03	gold quality
aorta	UBERON:0000947	82.69	gold quality
tibial artery	UBERON:0007610	82.48	gold quality
popliteal artery	UBERON:0002250	82.47	gold quality
body of uterus	UBERON:0009853	81.78	gold quality
buccal mucosa cell	CL:0002336	81.77	silver quality
endocervix	UBERON:0000458	81.49	gold quality
descending thoracic aorta	UBERON:0002345	81.22	gold quality
left coronary artery	UBERON:0001626	80.83	gold quality
right ovary	UBERON:0002118	80.46	gold quality
left ovary	UBERON:0002119	80.40	gold quality
colonic epithelium	UBERON:0000397	80.22	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	79.51	gold quality
metanephros	UBERON:0000081	79.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting EFCAB13, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-628-3P	99.04	68.37	814
HSA-MIR-3916	98.99	68.04	2155

Functional genomics

ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Efcab3	ENSMUSG00000020690
rattus_norvegicus	Efcab3	ENSRNOG00000042255

Protein

Protein identifiers

EF-hand calcium-binding domain-containing protein 13 — Q8IY85 (reviewed: Q8IY85)

All UniProt accessions (5): E5RFW6, E5RI18, Q8IY85, H0YBI2, K7ELL9

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IY85-1	1	yes
Q8IY85-2	2

RefSeq proteins (6): NP_001182121, NP_001413514, NP_001413515, NP_001413516, NP_001413517, NP_689560* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011992	EF-hand-dom_pair	Homologous_superfamily

UniProt features (17 total): domain 6, sequence variant 4, splice variant 3, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IY85-F1	53.37	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): TCANNTGAY_SREBP1_01, HMG20B_TARGET_GENES, HMGA1_TARGET_GENES, RBM34_TARGET_GENES, SALL4_TARGET_GENES, TFEB_TARGET_GENES, ZNF507_TARGET_GENES, ZNF610_TARGET_GENES, MIR1252_3P, MIR4427, MIR323A_3P, MIR561_5P, MIR637, MIR6875_5P, MIR3126_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

2085 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EFCAB13	CDRT15L2	A8MXV6	507
EFCAB13	FAM187B	Q17R55	479
EFCAB13	SLC22A24	Q8N4F4	478
EFCAB13	NPIPB8	E9PQR5	477
EFCAB13	OR10H5	Q8NGA6	464
EFCAB13	OR7G3	Q8NG95	446
EFCAB13	TBC1D28	Q2M2D7	445
EFCAB13	CCDC144A	A2RUR9	432
EFCAB13	OR10H1	Q9Y4A9	432
EFCAB13	NPIPB9	F8W1W9	431
EFCAB13	MAGEE2	Q8TD90	428
EFCAB13	TUFM	P49411	423
EFCAB13	LASP1	Q14847	422
EFCAB13	CEP41	Q9BYV8	420
EFCAB13	SYTL1	Q8IYJ3	420

IntAct

2 interactions, top by confidence:

A	B	Type	Score
EFCAB13	PPP1R10	psi-mi:“MI:0914”(association)	0.350

BioGRID (7): EFCAB13 (Affinity Capture-MS), PPP1R10 (Affinity Capture-MS), ZC3H4 (Affinity Capture-MS), NFS1 (Affinity Capture-MS), LYRM4 (Affinity Capture-MS), STX7 (Cross-Linking-MS (XL-MS)), EFCAB13 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0A6YYL3, A0A1B0GVN3, A1KXM5, A2AKX3, A2ARZ3, A2RUR9, A6NFE2, A6QR20, A7KBS4, A8MYB1, A9JSR5, D3ZNV2, E9Q7F5, H3BUK9, O75969, O77797, Q14BK3, Q15846, Q19UN5, Q29RU3, Q2YDE5, Q32L17, Q32MG2, Q3MJ40, Q3URS2, Q3ZRW6, Q3ZRW7, Q3ZRW9, Q4KLZ4, Q5CZC0, Q5IR70, Q5RBQ2, Q66HB6, Q6AXV6, Q6AXY9, Q7TPV2, Q810N5, Q86YR6, Q8IY85, Q8IYA2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	103
Likely benign	17
Benign	20

Top pathogenic / likely-pathogenic (0)

SpliceAI

5305 predictions. Top by Δscore:

Variant	Effect	Δscore
17:47326224:A:G	acceptor_gain	1.0000
17:47335354:AAT:A	donor_gain	1.0000
17:47335357:G:GG	donor_gain	1.0000
17:47345059:G:GT	donor_gain	1.0000
17:47345089:GAAT:G	donor_gain	1.0000
17:47345092:T:G	donor_gain	1.0000
17:47345092:T:TG	donor_gain	1.0000
17:47345096:GTG:G	donor_gain	1.0000
17:47361374:GCAGC:G	acceptor_loss	1.0000
17:47361375:CA:C	acceptor_loss	1.0000
17:47361376:A:AG	acceptor_gain	1.0000
17:47361376:AGCAT:A	acceptor_loss	1.0000
17:47361377:G:A	acceptor_loss	1.0000
17:47361377:G:GA	acceptor_gain	1.0000
17:47361377:GC:G	acceptor_gain	1.0000
17:47361377:GCA:G	acceptor_gain	1.0000
17:47361494:G:GT	donor_gain	1.0000
17:47361517:TGACA:T	donor_gain	1.0000
17:47361518:GACA:G	donor_gain	1.0000
17:47361518:GACAG:G	donor_gain	1.0000
17:47361519:ACA:A	donor_gain	1.0000
17:47361519:ACAG:A	donor_loss	1.0000
17:47361520:CA:C	donor_gain	1.0000
17:47361521:AG:A	donor_loss	1.0000
17:47361522:G:GG	donor_gain	1.0000
17:47361523:TGA:T	donor_loss	1.0000
17:47361524:GAGT:G	donor_loss	1.0000
17:47361525:AGT:A	donor_loss	1.0000
17:47361526:G:C	donor_loss	1.0000
17:47361527:T:G	donor_gain	1.0000

AlphaMissense

6541 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:47347871:T:C	L194P	0.959
17:47395897:T:C	L622P	0.953
17:47429881:T:C	L853P	0.951
17:47347831:T:C	F181L	0.950
17:47347833:T:A	F181L	0.950
17:47347833:T:G	F181L	0.950
17:47395944:T:C	F638L	0.948
17:47395946:T:A	F638L	0.948
17:47395946:T:G	F638L	0.948
17:47361426:T:A	V237D	0.947
17:47361401:T:C	F229L	0.942
17:47361403:C:A	F229L	0.942
17:47361403:C:G	F229L	0.942
17:47361423:G:C	R236P	0.941
17:47395945:T:C	F638S	0.940
17:47404618:T:C	F740L	0.929
17:47404620:T:A	F740L	0.929
17:47404620:T:G	F740L	0.929
17:47370485:T:C	L285P	0.928
17:47391512:T:C	L553P	0.918
17:47347819:G:C	A177P	0.912
17:47402158:T:C	F658L	0.912
17:47402160:T:A	F658L	0.912
17:47402160:T:G	F658L	0.912
17:47361380:T:C	F222L	0.911
17:47361382:C:A	F222L	0.911
17:47361382:C:G	F222L	0.911
17:47347931:T:C	L214P	0.908
17:47412844:G:C	A784P	0.901
17:47361453:T:C	L246S	0.899

dbSNP variants (sampled 300 via entrez): RS1000047742 (17:47414186 C>G), RS1000111537 (17:47392673 G>C), RS1000142051 (17:47382044 T>G), RS1000145254 (17:47355484 T>C,G), RS1000146014 (17:47406280 T>G), RS1000158887 (17:47336680 C>T), RS1000159518 (17:47356508 C>G), RS1000185859 (17:47351586 A>C), RS1000193776 (17:47359609 AT>A,ATT), RS1000213238 (17:47336986 A>G), RS1000244930 (17:47325969 A>G,T), RS1000265837 (17:47404204 G>A), RS1000291205 (17:47440273 G>T), RS1000320868 (17:47438583 G>C), RS1000367323 (17:47391731 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

13 associations (top):

Study	Trait	p-value
GCST002690_12	Very long-chain saturated fatty acid levels (fatty acid 20:0)	4.000000e-07
GCST005194_144	Coronary artery disease	4.000000e-06
GCST005951_16	Body mass index	4.000000e-08
GCST006479_99	Diverticular disease	2.000000e-06
GCST008391_4	Glaucoma (primary open-angle)	8.000000e-06
GCST008916_117	Asthma	1.000000e-09
GCST008939_2	Chromosomal aberration frequency (chromosome type) in genotoxic compound exposure	8.000000e-06
GCST008954_4	High chromosomal aberration frequency (chromosome type)	3.000000e-06
GCST009366_22	LDL cholesterol levels x long total sleep time interaction (2df test)	2.000000e-10
GCST010703_72	Brain morphology (MOSTest)	3.000000e-08
GCST011343_7	Body fat percentage and LDL-C (pairwise)	2.000000e-16
GCST90013466_19	Height	1.000000e-12
GCST90020028_1388	Hip circumference adjusted for BMI	2.000000e-11

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0006796	very long-chain saturated fatty acid measurement
EFO:0004340	body mass index
EFO:0009959	diverticular disease
EFO:0009861	chromosome-type aberration frequency
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004346	neuroimaging measurement
EFO:0007800	body fat percentage
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

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

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression, increases abundance, increases expression	3
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
4-aminophenylarsenoxide	decreases reaction, affects binding	1
Arsenic Trioxide	affects binding, decreases reaction	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases abundance, increases expression	1
Phthalic Acids	decreases expression	1
Triclosan	decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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