EFCAB10

Summary

EFCAB10 (EF-hand calcium binding domain 10, HGNC:34531) is a protein-coding gene on chromosome 7q22.3, encoding EF-hand calcium-binding domain-containing protein 10 (A6NFE3).

Predicted to enable calcium ion binding activity.

Source: NCBI Gene 100130771 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 401 total — 4 pathogenic
• MANE Select transcript: NM_001355526

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34531
Approved symbol	EFCAB10
Name	EF-hand calcium binding domain 10
Location	7q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000185055
Ensembl biotype	protein_coding
Entrez	100130771

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000460135, ENST00000469099, ENST00000480514, ENST00000485614, ENST00000486180, ENST00000490493, ENST00000930388

RefSeq mRNA: 5 — MANE Select: NM_001355526 NM_001355526, NM_001355527, NM_001355529, NM_001355530, NM_001355531

CCDS: CCDS87535, CCDS87536, CCDS87537, CCDS87538

Canonical transcript exons

ENST00000480514 — 5 exons

Exon	Start	End
ENSE00001866201	105581358	105581493
ENSE00001900386	105565124	105565447
ENSE00002033202	105567467	105567490
ENSE00003484558	105569407	105569571
ENSE00003569674	105569203	105569290

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 92.08.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9889 / max 166.7930, expressed in 255 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85440	0.6947	217
85443	0.1860	24
85442	0.0803	22
85441	0.0279	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	92.08	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.80	gold quality
left testis	UBERON:0004533	86.00	gold quality
testis	UBERON:0000473	85.93	gold quality
right testis	UBERON:0004534	85.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.42	gold quality
fallopian tube	UBERON:0003889	79.86	gold quality
endometrium	UBERON:0001295	72.02	gold quality
nucleus accumbens	UBERON:0001882	70.66	gold quality
caudate nucleus	UBERON:0001873	70.51	gold quality
right lung	UBERON:0002167	68.61	gold quality
hypothalamus	UBERON:0001898	68.47	gold quality
corpus callosum	UBERON:0002336	68.00	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.95	gold quality
superior frontal gyrus	UBERON:0002661	67.56	gold quality
Ammon’s horn	UBERON:0001954	67.04	gold quality
putamen	UBERON:0001874	66.81	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	66.23	gold quality
prefrontal cortex	UBERON:0000451	66.16	gold quality
brain	UBERON:0000955	66.11	gold quality
pituitary gland	UBERON:0000007	65.82	gold quality
cerebral cortex	UBERON:0000956	65.44	gold quality
granulocyte	CL:0000094	65.15	gold quality
lung	UBERON:0002048	64.99	gold quality
left uterine tube	UBERON:0001303	64.98	gold quality
cerebellar cortex	UBERON:0002129	64.92	gold quality
temporal lobe	UBERON:0001871	64.91	gold quality
cerebellar hemisphere	UBERON:0002245	64.86	gold quality
frontal cortex	UBERON:0001870	64.83	gold quality
cerebellum	UBERON:0002037	64.80	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.54
E-MTAB-9388	yes	6.46

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-42p14.3	ENSDARG00000092825
mus_musculus	Efcab10	ENSMUSG00000020562
rattus_norvegicus	Efcab10	ENSRNOG00000010730

Paralogs (1): TEX55 (ENSG00000163424)

Protein

Protein identifiers

EF-hand calcium-binding domain-containing protein 10 — A6NFE3 (reviewed: A6NFE3)

All UniProt accessions (6): A6NFE3, A0A2R8Y6P2, A0A2R8YDC4, C9J654, J3KR48, J3KR52

RefSeq proteins (5): NP_001342455, NP_001342456, NP_001342458, NP_001342459, NP_001342460 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR039879	EFC10	Family
IPR049760	DD_EFCAB10	Domain
IPR056587	EF_EFCAB10_C	Domain

Pfam: PF24548

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NFE3-F1	83.59	0.39

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): FOXN3_TARGET_GENES, ZNF507_TARGET_GENES, ZNF528_TARGET_GENES, ZNF618_TARGET_GENES, ZNF766_TARGET_GENES, ZSCAN31_TARGET_GENES, SAFB2_TARGET_GENES, GSE15659_NAIVE_VS_PTPRC_NEG_CD4_TCELL_UP, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_UP, GSE15659_NAIVE_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_NAIVE_CD4_TCELL_VS_ACTIVATED_TREG_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_RESTING_TREG_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_ACTIVATED_TREG_UP, chr7q22

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

464 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EFCAB10	TEX55	Q96M34	626
EFCAB10	STPG2	Q8N412	556
EFCAB10	DEFB125	Q8N687	516
EFCAB10	CATIP	Q7Z7H3	491
EFCAB10	CFAP206	Q8IYR0	488
EFCAB10	ROPN1B	Q9BZX4	475
EFCAB10	NT5C1B	Q96P26	471
EFCAB10	PRODH2	Q9UF12	449
EFCAB10	TPGS1	Q6ZTW0	448
EFCAB10	SH3YL1	Q96HL8	447
EFCAB10	RIIAD1	A6NNX1	447
EFCAB10	C8orf34	Q49A92	430
EFCAB10	TAFA1	Q7Z5A9	404
EFCAB10	DENND3	A2RUS2	399
EFCAB10	TP53I11	O14683	398

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6NFE3, B3LF48, C7A639, F1SSF9, I2DDG2, O13728, P02635, P02636, P05946, P08733, P14202, P32070, P45961, P81128, P83509, P97393, Q01449, Q02045, Q13017, Q3SZE5, Q3T064, Q4KLL5, Q4R6C5, Q4V7T8, Q52K82, Q54MF3, Q5E9G1, Q5R629, Q66IC9, Q6AXZ3, Q6DCF6, Q6DJ05, Q6NU25, Q803V3, Q91YM2, Q94CF0, Q969Q6, Q96C74, Q9BZX4, Q9D581

Diamond homologs: A6NFE3, Q9D581

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	255
Likely benign	119
Benign	4

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
1047352	NM_021930.6(RINT1):c.1998_1999del (p.Cys667fs)	Pathogenic
1430736	NM_021930.6(RINT1):c.2021del (p.Phe674fs)	Pathogenic
1468558	NM_021930.6(RINT1):c.2087del (p.Phe696fs)	Pathogenic
970398	NM_021930.6(RINT1):c.2047_2050dup (p.Val684fs)	Pathogenic

SpliceAI

620 predictions. Top by Δscore:

Variant	Effect	Δscore
7:105565273:CCAG:C	acceptor_loss	1.0000
7:105565274:CA:C	acceptor_loss	1.0000
7:105565275:A:AG	acceptor_gain	1.0000
7:105565275:AGAT:A	acceptor_gain	1.0000
7:105565275:AGATG:A	acceptor_gain	1.0000
7:105565276:G:GA	acceptor_gain	1.0000
7:105565276:G:GT	acceptor_loss	1.0000
7:105565276:GA:G	acceptor_gain	1.0000
7:105565276:GAT:G	acceptor_gain	1.0000
7:105565276:GATG:G	acceptor_gain	1.0000
7:105565276:GATGG:G	acceptor_gain	1.0000
7:105565458:G:GG	donor_gain	1.0000
7:105565529:GATA:G	acceptor_gain	1.0000
7:105565646:ACA:A	donor_gain	1.0000
7:105565647:CA:C	donor_gain	1.0000
7:105565649:G:GG	donor_gain	1.0000
7:105567113:A:AG	acceptor_gain	1.0000
7:105567115:ACAGT:A	acceptor_loss	1.0000
7:105567116:CAGTA:C	acceptor_loss	1.0000
7:105567117:A:AG	acceptor_gain	1.0000
7:105567118:G:GA	acceptor_gain	1.0000
7:105567118:GT:G	acceptor_gain	1.0000
7:105567118:GTA:G	acceptor_gain	1.0000
7:105567118:GTAT:G	acceptor_gain	1.0000
7:105567118:GTATA:G	acceptor_gain	1.0000
7:105569196:AACTT:A	donor_loss	1.0000
7:105569197:ACTTA:A	donor_loss	1.0000
7:105569199:TTAC:T	donor_loss	1.0000
7:105569200:T:TG	donor_loss	1.0000
7:105569201:A:AC	donor_gain	1.0000

AlphaMissense

845 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:105569462:A:C	F72L	0.965
7:105569462:A:T	F72L	0.965
7:105569464:A:G	F72L	0.965
7:105569430:A:T	I83K	0.964
7:105569214:G:C	F116L	0.954
7:105569214:G:T	F116L	0.954
7:105569216:A:G	F116L	0.954
7:105569215:A:G	F116S	0.950
7:105569407:C:G	A91P	0.943
7:105569430:A:C	I83R	0.935
7:105569287:A:G	L92P	0.930
7:105581368:G:C	F32L	0.923
7:105581368:G:T	F32L	0.923
7:105581370:A:G	F32L	0.923
7:105569524:C:G	A52P	0.918
7:105581427:A:G	Y13H	0.917
7:105581426:T:G	Y13S	0.913
7:105581387:A:G	L26P	0.912
7:105581375:A:G	L30P	0.907
7:105569541:A:G	L46S	0.905
7:105581436:C:G	A10P	0.905
7:105569272:A:G	L97P	0.900
7:105569452:C:G	D76H	0.899
7:105569544:A:G	L45P	0.897
7:105569553:A:G	L42S	0.897
7:105581415:G:C	H17D	0.894
7:105569477:G:C	N67K	0.893
7:105569477:G:T	N67K	0.893
7:105569532:A:G	L49P	0.893
7:105581408:A:G	I19T	0.891

dbSNP variants (sampled 300 via entrez): RS1000091416 (7:105583026 T>C), RS1000245564 (7:105574662 A>AT), RS1000279432 (7:105576212 T>G), RS1000416561 (7:105580504 G>C), RS1000483997 (7:105579422 T>C), RS1000496011 (7:105568729 A>G), RS1000592399 (7:105573127 T>C), RS1000704301 (7:105579116 C>T), RS1000955944 (7:105569466 A>G), RS1001271394 (7:105575159 T>C), RS1001542854 (7:105571288 G>T), RS1001575370 (7:105577474 C>A,G,T), RS1001643140 (7:105581652 T>G), RS1001659045 (7:105571698 C>T), RS1001922896 (7:105577783 A>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:618641

GenCC curated gene-disease

Mondo (1): infantile liver failure syndrome 3 (MONDO:0032844)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	decreases methylation	1
beta-lapachone	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Estradiol	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1
Permethrin	decreases expression	1

Clinical trials (associated diseases)

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