YAE1

Summary

YAE1 (YAE1 maturation factor of ABCE1, HGNC:24857) is a protein-coding gene on chromosome 7p14.1, encoding Protein YAE1 homolog (Q9NRH1). The complex LTO1:YAE1 functions as a target specific adapter that probably recruits apo-ABCE1 to the cytosolic iron-sulfur protein assembly (CIA) complex machinery. It is a common-essential gene (DepMap: required in 94.8% of cancer cell lines).

Predicted to be located in cytoplasm and nucleus.

Source: NCBI Gene 57002 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 26 total
• Cancer dependency (DepMap): dependent in 94.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_020192

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24857
Approved symbol	YAE1
Name	YAE1 maturation factor of ABCE1
Location	7p14.1
Locus type	gene with protein product
Status	Approved
Aliases	GK003, CIAB2
Ensembl gene	ENSG00000241127
Ensembl biotype	protein_coding
Entrez	57002

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000223273, ENST00000432096, ENST00000448268, ENST00000469737, ENST00000474392, ENST00000485025, ENST00000895141, ENST00000922528

RefSeq mRNA: 2 — MANE Select: NM_020192 NM_001282446, NM_020192

CCDS: CCDS5459, CCDS64630

Canonical transcript exons

ENST00000223273 — 3 exons

Exon	Start	End
ENSE00000832450	39572277	39572881
ENSE00001863777	39566404	39566547
ENSE00002075122	39570506	39570627

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 92.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.3785 / max 664.7939, expressed in 1777 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
78245	17.4278	1772
78246	0.9507	503

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	92.91	gold quality
calcaneal tendon	UBERON:0003701	92.70	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.30	gold quality
ileal mucosa	UBERON:0000331	91.87	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.59	gold quality
ganglionic eminence	UBERON:0004023	91.23	gold quality
cardiac muscle of right atrium	UBERON:0003379	91.19	gold quality
rectum	UBERON:0001052	91.01	gold quality
left ovary	UBERON:0002119	90.82	gold quality
right uterine tube	UBERON:0001302	90.43	gold quality
kidney epithelium	UBERON:0004819	90.42	silver quality
islet of Langerhans	UBERON:0000006	90.37	gold quality
myocardium	UBERON:0002349	90.16	gold quality
adenohypophysis	UBERON:0002196	90.14	gold quality
ventricular zone	UBERON:0003053	90.08	gold quality
body of uterus	UBERON:0009853	90.04	gold quality
pituitary gland	UBERON:0000007	89.95	gold quality
endocervix	UBERON:0000458	89.75	gold quality
right ovary	UBERON:0002118	89.72	gold quality
ovary	UBERON:0000992	89.62	gold quality
tendon	UBERON:0000043	89.50	gold quality
mucosa of transverse colon	UBERON:0004991	89.41	gold quality
cerebellar hemisphere	UBERON:0002245	89.34	gold quality
cerebellar cortex	UBERON:0002129	89.32	gold quality
mucosa of sigmoid colon	UBERON:0004993	89.26	gold quality
smooth muscle tissue	UBERON:0001135	89.12	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.09	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.03	gold quality
small intestine Peyer’s patch	UBERON:0003454	88.84	gold quality
muscle layer of sigmoid colon	UBERON:0035805	88.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting YAE1, 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-656-3P	100.00	72.15	2788
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-2053	99.57	69.15	1635
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-633	98.35	69.45	1167
HSA-MIR-4712-5P	97.24	67.79	775
HSA-MIR-770-5P	97.24	68.10	758

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 94.8% of screened cell lines, common-essential.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	otulina	ENSDARG00000045422
mus_musculus	Yae1d1	ENSMUSG00000075054
rattus_norvegicus	Yae1l1	ENSRNOG00000008962
rattus_norvegicus	Yae1	ENSRNOG00000013438

Protein

Protein identifiers

Protein YAE1 homolog — Q9NRH1 (reviewed: Q9NRH1)

Alternative names: Yae1 domain-containing protein 1

All UniProt accessions (2): Q9NRH1, C9IZ57

UniProt curated annotations — full annotation on UniProt →

Function. The complex LTO1:YAE1 functions as a target specific adapter that probably recruits apo-ABCE1 to the cytosolic iron-sulfur protein assembly (CIA) complex machinery. May be required for biogenesis of the large ribosomal subunit and initiation of translation.

Subunit / interactions. Forms a complex with LTO1.

Subcellular location. Cytoplasm. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NRH1-1	1	yes
Q9NRH1-2	2

RefSeq proteins (2): NP_001269375, NP_064577* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019191	Essential_protein_Yae1_N	Domain
IPR038881	Yae1-like	Family

Pfam: PF09811

UniProt features (8 total): sequence conflict 3, splice variant 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRH1-F1	70.96	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_PROTEIN_MATURATION, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, TGANTCA_AP1_C, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, ACEVEDO_LIVER_CANCER_UP, SANSOM_APC_MYC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, NAKAMURA_ADIPOGENESIS_LATE_UP, CHYLA_CBFA2T3_TARGETS_DN, LEE_BMP2_TARGETS_DN, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN

GO Biological Process (1): protein maturation (GO:0051604)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
protein metabolic process	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

392 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YAE1	LTO1	Q8WV07	745
YAE1	ABCE1	P61221	687
YAE1	CIAO3	Q9H6Q4	657
YAE1	MMS19	Q96T76	647
YAE1	NUBP1	P53384	625
YAE1	CIAPIN1	Q6FI81	606
YAE1	ZC3H4	Q9UPT8	504
YAE1	CIAO1	O76071	499
YAE1	KHDC4	Q7Z7F0	471
YAE1	NFS1	Q9Y697	464
YAE1	NUBPL	Q8TB37	459
YAE1	OR14J1	Q9UGF5	447
YAE1	ABCB7	O75027	431
YAE1	NFU1	Q9UMS0	423
YAE1	OR2J2	O76002	418

IntAct

43 interactions, top by confidence:

A	B	Type	Score
EXOC7	YAE1	psi-mi:“MI:0915”(physical association)	0.560
LTO1	YAE1	psi-mi:“MI:0915”(physical association)	0.560
YAE1	EXOC7	psi-mi:“MI:0915”(physical association)	0.560
YAE1	CHD3	psi-mi:“MI:0915”(physical association)	0.550
YAE1	CEP126	psi-mi:“MI:0915”(physical association)	0.550
VIM	YAE1	psi-mi:“MI:0915”(physical association)	0.550
ABCE1	EIF3H	psi-mi:“MI:0914”(association)	0.530
YAE1		psi-mi:“MI:0915”(physical association)	0.370
YAE1	BBS10	psi-mi:“MI:0915”(physical association)	0.370
YAE1	METTL18	psi-mi:“MI:0915”(physical association)	0.370
CRMP1	YAE1	psi-mi:“MI:0915”(physical association)	0.370
HNRNPA2B1	YAE1	psi-mi:“MI:0915”(physical association)	0.370
YAE1	HAUS5	psi-mi:“MI:0915”(physical association)	0.370
MCF2L	YAE1	psi-mi:“MI:0915”(physical association)	0.370
NACAD	YAE1	psi-mi:“MI:0915”(physical association)	0.370
YAE1	NAT14	psi-mi:“MI:0915”(physical association)	0.370
SERPINA4	YAE1	psi-mi:“MI:0915”(physical association)	0.370
SLC25A33	YAE1	psi-mi:“MI:0915”(physical association)	0.370
ZNF579	YAE1	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
COPS5	FBLL1	psi-mi:“MI:0914”(association)	0.350
CUL2	ANXA2P2	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
USP53	ANXA2P2	psi-mi:“MI:0914”(association)	0.350
L	MYO1C	psi-mi:“MI:0914”(association)	0.350
MAP1LC3A		psi-mi:“MI:0914”(association)	0.350
MAP1LC3B		psi-mi:“MI:0914”(association)	0.350
GABARAPL2		psi-mi:“MI:0914”(association)	0.350

BioGRID (36): YAE1D1 (Affinity Capture-MS), YAE1D1 (Affinity Capture-MS), YAE1D1 (Two-hybrid), VIM (Two-hybrid), YAE1D1 (Two-hybrid), CHD3 (Two-hybrid), KIAA1377 (Two-hybrid), YAE1D1 (Two-hybrid), YAE1D1 (Two-hybrid), YAE1D1 (Negative Genetic), YAE1D1 (Negative Genetic), YAE1D1 (Affinity Capture-MS), YAE1D1 (Affinity Capture-MS), YAE1D1 (Affinity Capture-MS), YAE1D1 (Affinity Capture-MS)

ESM2 similar proteins: A5E625, A6NKT7, A6QR20, A7E379, A8KBE0, B0S6S9, B3LW62, B4F6Q9, O13889, O14715, O14981, O60281, O73622, O74331, O74485, O95397, P0C8Y6, P0DJD0, P0DJD1, P40960, Q06190, Q08119, Q08215, Q08C99, Q0V9S3, Q0VF22, Q1X8D7, Q501X2, Q504Y3, Q5RA75, Q64EW0, Q6ZQ93, Q70CQ2, Q7TPV2, Q7Z3J3, Q86Y13, Q8BPY9, Q8C0P7, Q8RWM3, Q95JJ5

Diamond homologs: A3LWJ7, A4RK96, A5DLN4, A5E625, A6ZQ26, A7TE16, O14045, P47118, Q6BL68, Q6C531, Q6CV86, Q6FUV0, Q753A3, Q9NRH1, Q9P840

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 35 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Macroautophagy	5	26.2×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
autophagosome maturation	5	56.6×	3e-06
mitophagy	5	51.3×	3e-06
autophagosome assembly	5	36.2×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

449 predictions. Top by Δscore:

Variant	Effect	Δscore
7:39566523:GA:G	donor_gain	1.0000
7:39566525:G:GG	donor_gain	1.0000
7:39566543:TCA:T	donor_gain	1.0000
7:39566548:G:GG	donor_gain	1.0000
7:39570505:GGAA:G	acceptor_gain	0.9900
7:39570623:TTGAG:T	donor_loss	0.9900
7:39570624:TGAGG:T	donor_loss	0.9900
7:39570625:GAGG:G	donor_loss	0.9900
7:39570626:AG:A	donor_loss	0.9900
7:39570627:GG:G	donor_loss	0.9900
7:39570628:G:A	donor_loss	0.9900
7:39570629:T:A	donor_loss	0.9900
7:39572275:A:AG	acceptor_gain	0.9900
7:39572276:G:GG	acceptor_gain	0.9900
7:39566516:A:T	donor_gain	0.9800
7:39566537:G:GT	donor_gain	0.9800
7:39566538:A:G	donor_gain	0.9800
7:39572276:GT:G	acceptor_gain	0.9800
7:39570503:TA:T	acceptor_loss	0.9700
7:39570504:A:AG	acceptor_gain	0.9700
7:39570505:G:GG	acceptor_gain	0.9700
7:39566515:G:GT	donor_gain	0.9600
7:39566524:A:AG	donor_gain	0.9600
7:39570505:GGA:G	acceptor_gain	0.9600
7:39572276:GTGCT:G	acceptor_gain	0.9600
7:39566470:G:T	donor_gain	0.9500
7:39566528:ACAT:A	donor_gain	0.9500
7:39566537:GACGA:G	donor_gain	0.9500
7:39570583:TGCAG:T	donor_gain	0.9500
7:39572275:AGT:A	acceptor_gain	0.9500

AlphaMissense

1488 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:39570560:T:C	F62L	0.989
7:39570562:C:A	F62L	0.989
7:39570562:C:G	F62L	0.989
7:39570561:T:C	F62S	0.987
7:39570572:T:G	Y66D	0.980
7:39566476:T:C	F20L	0.979
7:39566478:T:A	F20L	0.979
7:39566478:T:G	F20L	0.979
7:39570617:G:A	G81R	0.977
7:39570617:G:C	G81R	0.977
7:39572279:C:A	A85D	0.977
7:39572278:G:C	A85P	0.972
7:39572342:T:C	L106P	0.972
7:39570530:G:C	A52P	0.970
7:39570509:G:C	G45R	0.968
7:39570512:T:G	Y46D	0.965
7:39570569:G:C	G65R	0.965
7:39570618:G:A	G81E	0.963
7:39566518:T:A	W34R	0.962
7:39566518:T:C	W34R	0.962
7:39570522:G:A	G49E	0.962
7:39570534:G:A	G53D	0.962
7:39570549:T:C	L58P	0.962
7:39570615:G:C	R80P	0.962
7:39570573:A:C	Y66S	0.957
7:39566540:G:C	R41P	0.955
7:39570584:G:C	A70P	0.953
7:39570581:G:C	G69R	0.952
7:39570510:G:A	G45D	0.947
7:39570570:G:A	G65D	0.946

dbSNP variants (sampled 300 via entrez): RS1000106247 (7:39574600 G>A), RS1000171925 (7:39571467 TG>T), RS1000204464 (7:39571202 C>G), RS1000313582 (7:39577507 G>A), RS1000356529 (7:39589825 C>T), RS1000368182 (7:39606192 A>T), RS1000440252 (7:39583200 A>G,T), RS1000541360 (7:39575546 G>A,C), RS1000657143 (7:39608135 T>C), RS1000704277 (7:39607541 T>C), RS1000747339 (7:39565088 A>C), RS1000776321 (7:39607241 A>C,G), RS1001127000 (7:39594615 T>C), RS1001175223 (7:39577545 G>T), RS1001205347 (7:39596315 C>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
GCST007327_74	Smoking status (ever vs never smokers)	4.000000e-08
GCST009964_1	Opioid use disorder	1.000000e-08
GCST009964_2	Opioid use disorder	1.000000e-08
GCST010219_10	Attention deficit hyperactivity disorder (inattention symptoms)	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004318	smoking behavior
EFO:0010702	opioid use disorder

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
salinomycin	decreases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
cylindrospermopsin	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
perfluorohexanesulfonic acid	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Atrazine	decreases expression	1
Lead	affects expression	1
Oxygen	decreases expression	1
Quercetin	decreases expression	1
Smoke	decreases expression, increases abundance	1
Urethane	decreases expression	1
Valproic Acid	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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