ELP5

Summary

ELP5 (elongator acetyltransferase complex subunit 5, HGNC:30617) is a protein-coding gene on chromosome 17p13.1, encoding Elongator complex protein 5 (Q8TE02). Component of the elongator complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine). It is a common-essential gene (DepMap: required in 94.3% of cancer cell lines).

Predicted to contribute to tRNA binding activity. Predicted to be involved in positive regulation of cell migration and tRNA modification. Located in cytosol and nucleoplasm. Part of elongator holoenzyme complex.

Source: NCBI Gene 23587 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 76 total
• Cancer dependency (DepMap): dependent in 94.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_203414

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30617
Approved symbol	ELP5
Name	elongator acetyltransferase complex subunit 5
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Aliases	DERP6
Ensembl gene	ENSG00000170291
Ensembl biotype	protein_coding
OMIM	615019
Entrez	23587

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 25 protein_coding, 1 nonsense_mediated_decay

ENST00000354429, ENST00000356683, ENST00000396627, ENST00000396628, ENST00000570322, ENST00000570500, ENST00000571146, ENST00000572104, ENST00000573657, ENST00000573699, ENST00000574255, ENST00000574841, ENST00000574993, ENST00000576496, ENST00000715856, ENST00000888421, ENST00000888422, ENST00000888423, ENST00000888424, ENST00000888425, ENST00000888426, ENST00000888427, ENST00000912605, ENST00000964723, ENST00000964724, ENST00000964725

RefSeq mRNA: 4 — MANE Select: NM_203414 NM_015362, NM_203413, NM_203414, NM_203415

CCDS: CCDS11094, CCDS11095

Canonical transcript exons

ENST00000396628 — 8 exons

Exon	Start	End
ENSE00001150307	7254583	7254803
ENSE00001278052	7252770	7252830
ENSE00001333802	7258826	7258926
ENSE00001333803	7258588	7258683
ENSE00001403709	7259571	7259937
ENSE00003510297	7252918	7252998
ENSE00003651663	7256857	7257038
ENSE00003732639	7252215	7252596

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.0463 / max 313.9551, expressed in 1819 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159127	20.2698	1812
159126	7.7534	1722
159125	3.6062	1548
159123	0.2488	93
159124	0.1681	59

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	98.51	gold quality
left testis	UBERON:0004533	98.41	gold quality
testis	UBERON:0000473	97.22	gold quality
apex of heart	UBERON:0002098	97.12	gold quality
mucosa of transverse colon	UBERON:0004991	95.61	gold quality
heart left ventricle	UBERON:0002084	93.64	gold quality
smooth muscle tissue	UBERON:0001135	93.12	gold quality
right adrenal gland	UBERON:0001233	92.98	gold quality
right adrenal gland cortex	UBERON:0035827	92.97	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.91	gold quality
ventricular zone	UBERON:0003053	92.88	gold quality
granulocyte	CL:0000094	92.82	gold quality
right lobe of liver	UBERON:0001114	92.79	gold quality
left adrenal gland cortex	UBERON:0035825	92.79	gold quality
left adrenal gland	UBERON:0001234	92.69	gold quality
gastrocnemius	UBERON:0001388	92.65	gold quality
prefrontal cortex	UBERON:0000451	92.61	gold quality
heart	UBERON:0000948	92.55	gold quality
muscle of leg	UBERON:0001383	92.51	gold quality
right atrium auricular region	UBERON:0006631	92.49	gold quality
ganglionic eminence	UBERON:0004023	92.29	gold quality
frontal cortex	UBERON:0001870	91.84	gold quality
pituitary gland	UBERON:0000007	91.79	gold quality
adrenal gland	UBERON:0002369	91.65	gold quality
anterior cingulate cortex	UBERON:0009835	91.47	gold quality
adenohypophysis	UBERON:0002196	91.45	gold quality
cerebral cortex	UBERON:0000956	91.34	gold quality
muscle layer of sigmoid colon	UBERON:0035805	91.09	gold quality
right frontal lobe	UBERON:0002810	91.07	gold quality
liver	UBERON:0002107	91.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.88

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF

miRNA regulators (miRDB)

6 targeting ELP5, 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-7110-3P	100.00	73.18	2486
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-12125	98.59	67.54	1044
HSA-MIR-152-5P	96.42	66.59	960

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 94.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• cloning and characterization of the DERP6 gene, isolated from testis cDNA library; results indicate that the DERP6 may be involved in p53-mediated gene transcription (PMID:16850183)
• data identify DERP6/ELP5 and C3ORF75/ELP6 as key players for migration, invasion and tumorigenicity of melanoma cells, as integral subunits of Elongator. (PMID:22854966)
• Loss of ELP5 impairs the integrity and stability of the Elongator complex to abrogate wobble U34 tRNA modification, and directly impedes the wobble U34 modification-dependent translation of hnRNPQ mRNA. (PMID:31792210)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	elp5	ENSDARG00000067918
mus_musculus	Elp5	ENSMUSG00000018565
rattus_norvegicus	Elp5	ENSRNOG00000027628

Protein

Protein identifiers

Elongator complex protein 5 — Q8TE02 (reviewed: Q8TE02)

Alternative names: Dermal papilla-derived protein 6, S-phase 2 protein

All UniProt accessions (8): Q8TE02, I3L1A8, I3L1Q3, I3L200, I3L2A9, I3L2T0, I3L437, I3NI50

UniProt curated annotations — full annotation on UniProt →

Function. Component of the elongator complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine). The elongator complex catalyzes formation of carboxymethyluridine in the wobble base at position 34 in tRNAs. Involved in cell migration.

Subunit / interactions. Component of the elongator complex which consists of ELP1, ELP2, ELP3, ELP4, ELP5 and ELP6; in the complex, is required for optimal binding of ELP3 to ELP4.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Ubiquitously expressed with high levels in heart, brain, liver, skeletal muscle and testis.

Post-translational modifications. Tyrosine-phosphorylated.

Pathway. tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis.

Miscellaneous. Produced by alternative initiation at Met-1 of isoform 5. Major isoform.

Similarity. Belongs to the ELP5 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8TE02-5	5	yes
Q8TE02-1	1
Q8TE02-2	2
Q8TE02-3	3

RefSeq proteins (4): NP_056177, NP_981958, NP_981959, NP_981960 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019519	Elp5	Family

Pfam: PF10483

UniProt features (17 total): sequence conflict 6, splice variant 5, sequence variant 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TE02-F1	79.14	0.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 252

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-3214847	HATs acetylate histones

MSigDB gene sets: 148 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, AAGTCCA_MIR422B_MIR422A, LFA1_Q6, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_TRNA_METABOLIC_PROCESS, TAL1ALPHAE47_01, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_RNA_MODIFICATION, GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, PETRETTO_CARDIAC_HYPERTROPHY, RYTTCCTG_ETS2_B, FISCHER_DREAM_TARGETS, LINDVALL_IMMORTALIZED_BY_TERT_DN

GO Biological Process (5): tRNA wobble uridine modification (GO:0002098), tRNA modification (GO:0006400), regulation of translation (GO:0006417), positive regulation of cell migration (GO:0030335), tRNA processing (GO:0008033)

GO Molecular Function (2): tRNA binding (GO:0000049), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), elongator holoenzyme complex (GO:0033588)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Chromatin modifying enzymes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
tRNA wobble base modification	1
tRNA processing	1
RNA modification	1
translation	1
post-transcriptional regulation of gene expression	1
regulation of protein metabolic process	1
cell migration	1
regulation of cell migration	1
positive regulation of cell motility	1
RNA processing	1
tRNA metabolic process	1
RNA binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
intracellular protein-containing complex	1
catalytic complex	1

Protein interactions and networks

STRING

1136 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ELP5	ELP4	Q96EB1	991
ELP5	ELP2	Q6IA86	982
ELP5	ELP6	Q0PNE2	980
ELP5	ELP3	Q9H9T3	914
ELP5	ELP1	O95163	737
ELP5	CTU1	Q7Z7A3	667
ELP5	DPH3	Q96FX2	607
ELP5	DPH2	Q9BQC3	588
ELP5	GHITM	Q9H3K2	571
ELP5	KTI12	Q96EK9	564
ELP5	MOCS3	O95396	551
ELP5	DPH5	Q9H2P9	551
ELP5	MCM5	P33992	519
ELP5	DPH1	Q9BZG8	515
ELP5	CTU2	Q2VPK5	502

IntAct

29 interactions, top by confidence:

A	B	Type	Score
ELP3	ELP1	psi-mi:“MI:0914”(association)	0.840
ATXN1	ELP5	psi-mi:“MI:0915”(physical association)	0.700
ELP5	ATXN1	psi-mi:“MI:0915”(physical association)	0.700
ELP4	ELP5	psi-mi:“MI:0915”(physical association)	0.620
ELP4	ELP1	psi-mi:“MI:0914”(association)	0.600
ELP5	ELP6	psi-mi:“MI:0915”(physical association)	0.560
PIPOX	ZNF217	psi-mi:“MI:0914”(association)	0.530
ELP1	ELP5	psi-mi:“MI:0914”(association)	0.460
ELP5	ELP1	psi-mi:“MI:0914”(association)	0.460
APBA1	KIF2A	psi-mi:“MI:0914”(association)	0.350
ELP4	HSPA8	psi-mi:“MI:0914”(association)	0.350
ELP6	ZBTB25	psi-mi:“MI:0914”(association)	0.350
KLHL15	PPIA	psi-mi:“MI:0914”(association)	0.350
ELP3	ACACB	psi-mi:“MI:0914”(association)	0.350
ELP6	ELP2	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350
SSU72	PCF11	psi-mi:“MI:2364”(proximity)	0.270
ATXN1	ELP5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (36): ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-Western), ELP5 (Reconstituted Complex), ELP5 (Proximity Label-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-RNA), ELP5 (Proximity Label-MS), ELP5 (Proximity Label-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-MS), ELP5 (Affinity Capture-MS)

ESM2 similar proteins: A1L134, A9ULG4, B1H1N7, B2RUP2, D3ZI76, D3ZUM2, F1MLB4, I3L5V6, O95870, P47823, P70295, Q13144, Q14DK4, Q16586, Q1HAQ0, Q1JPD2, Q1LWG4, Q27J81, Q2TBP5, Q3TFD2, Q4R8P0, Q5NVK5, Q5R6S0, Q64350, Q643R3, Q6MG55, Q6NUI2, Q6NVG1, Q6PBN5, Q6PDS3, Q6SZW1, Q6V7V2, Q70J99, Q7TN37, Q8CHW4, Q8N0W3, Q8N9W5, Q8NF37, Q8TE02, Q95K25

Diamond homologs: A1A5V9, Q24050, Q6IUP3, Q8TE02, Q99L85

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ELP5	“form complex”	“Elongator complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 18 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
HATs acetylate histones	5	26.4×	8e-05

GO biological processes:

GO term	Partners	Fold	FDR
regulation of translation	5	60.8×	1e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	5
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1144 predictions. Top by Δscore:

Variant	Effect	Δscore
17:7251189:GCTCA:G	donor_loss	1.0000
17:7251190:CTCA:C	donor_loss	1.0000
17:7251192:CA:C	donor_loss	1.0000
17:7251193:ACCGT:A	donor_loss	1.0000
17:7252593:CGGG:C	donor_loss	1.0000
17:7252594:GGG:G	donor_gain	1.0000
17:7252595:GG:G	donor_gain	1.0000
17:7252595:GGG:G	donor_gain	1.0000
17:7252596:GG:G	donor_gain	1.0000
17:7252597:GT:G	donor_loss	1.0000
17:7252598:T:G	donor_loss	1.0000
17:7252760:C:CA	acceptor_gain	1.0000
17:7252765:TGCAG:T	acceptor_loss	1.0000
17:7252766:GCAGA:G	acceptor_loss	1.0000
17:7252767:CA:C	acceptor_loss	1.0000
17:7252768:A:AG	acceptor_gain	1.0000
17:7252768:AGATT:A	acceptor_loss	1.0000
17:7252769:G:GA	acceptor_gain	1.0000
17:7252826:CTGTG:C	donor_gain	1.0000
17:7252828:GTG:G	donor_gain	1.0000
17:7252829:TG:T	donor_gain	1.0000
17:7252830:GG:G	donor_gain	1.0000
17:7252831:G:GG	donor_gain	1.0000
17:7252832:T:A	donor_loss	1.0000
17:7252833:GAGTA:G	donor_loss	1.0000
17:7252916:A:AG	acceptor_gain	1.0000
17:7252916:AGT:A	acceptor_gain	1.0000
17:7252916:AGTG:A	acceptor_gain	1.0000
17:7252916:AGTGG:A	acceptor_gain	1.0000
17:7252917:G:GT	acceptor_gain	1.0000

AlphaMissense

2054 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:7254725:A:C	S127R	0.992
17:7254727:C:A	S127R	0.992
17:7254727:C:G	S127R	0.992
17:7258850:T:C	F254L	0.978
17:7258852:T:A	F254L	0.978
17:7258852:T:G	F254L	0.978
17:7258907:T:C	F273L	0.974
17:7258909:C:A	F273L	0.974
17:7258909:C:G	F273L	0.974
17:7254719:T:C	S125P	0.963
17:7252787:G:T	G38W	0.959
17:7252812:T:A	V46D	0.959
17:7254726:G:T	S127I	0.958
17:7252787:G:A	G38R	0.957
17:7252787:G:C	G38R	0.957
17:7254711:C:A	A122D	0.957
17:7252804:G:C	K43N	0.952
17:7252804:G:T	K43N	0.952
17:7252596:G:C	D32H	0.949
17:7254716:G:C	D124H	0.949
17:7252965:T:C	F68S	0.944
17:7252964:T:C	F68L	0.943
17:7252966:T:A	F68L	0.943
17:7252966:T:G	F68L	0.943
17:7256893:G:A	G165D	0.942
17:7258913:T:C	F275L	0.942
17:7258915:C:A	F275L	0.942
17:7258915:C:G	F275L	0.942
17:7256892:G:C	G165R	0.938
17:7254723:T:G	L126R	0.936

dbSNP variants (sampled 300 via entrez): RS1000038770 (17:7256063 TAAA>T), RS1000925641 (17:7250300 T>C), RS1001008709 (17:7260316 C>G,T), RS1001609662 (17:7259081 C>A), RS1001815552 (17:7253480 G>A), RS1002093312 (17:7253617 T>A), RS1002161901 (17:7253714 G>C,T), RS1002203790 (17:7257853 A>C), RS1002759635 (17:7255159 T>C), RS1003206825 (17:7259198 T>C), RS1003609684 (17:7256586 C>T), RS1003684242 (17:7250009 G>A), RS1004021333 (17:7251346 G>T), RS1004073932 (17:7251514 G>A,T), RS1004103045 (17:7251954 C>G,T)

Disease associations

OMIM: gene MIM:615019 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

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)

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs4562	Efficacy	3	methylphenidate	Attention Deficit Disorder with Hyperactivity

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs4562	CLDN7, ELP5	3	0.00	1	methylphenidate

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	5
aristolochic acid I	increases expression	1
testosterone enanthate	affects expression	1
alpha-pinene	increases expression, increases oxidation, increases abundance, affects cotreatment	1
beta-lapachone	decreases expression	1
sodium arsenite	decreases expression, increases abundance	1
cobaltous chloride	decreases expression	1
methacrylaldehyde	increases abundance, affects cotreatment, increases expression, increases oxidation	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
Bortezomib	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic Trioxide	increases expression	1
Leflunomide	decreases expression	1
Acrolein	affects cotreatment, increases expression, increases oxidation, increases abundance	1
Air Pollutants	increases abundance, increases expression, increases oxidation, affects cotreatment	1
Arsenic	decreases expression, increases abundance	1
Cadmium	increases abundance, increases expression	1
Coumestrol	increases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Ivermectin	decreases expression	1
Ozone	increases oxidation, increases abundance, affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Volatile Organic Compounds	affects cotreatment, increases expression, increases oxidation	1

Clinical trials (associated diseases)

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