MRPL27

Summary

MRPL27 (mitochondrial ribosomal protein L27, HGNC:14483) is a protein-coding gene on chromosome 17q21.33, encoding Large ribosomal subunit protein bL27m (Q9P0M9). It is a selective cancer dependency (DepMap: 81.5% of cell lines).

Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein.

Source: NCBI Gene 51264 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 22 total
• Cancer dependency (DepMap): dependent in 81.5% of screened cell lines
• MANE Select transcript: NM_016504

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14483
Approved symbol	MRPL27
Name	mitochondrial ribosomal protein L27
Location	17q21.33
Locus type	gene with protein product
Status	Approved
Aliases	bL27m
Ensembl gene	ENSG00000108826
Ensembl biotype	protein_coding
OMIM	611837
Entrez	51264

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000225969, ENST00000442592, ENST00000503633, ENST00000507088, ENST00000508200, ENST00000511860, ENST00000514928, ENST00000928292

RefSeq mRNA: 1 — MANE Select: NM_016504 NM_016504

CCDS: CCDS11564

Canonical transcript exons

ENST00000225969 — 4 exons

Exon	Start	End
ENSE00000737034	50370032	50370099
ENSE00002021904	50367867	50368298
ENSE00002037808	50373131	50373184
ENSE00003664247	50370455	50370586

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 97.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.6509 / max 292.7918, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166975	38.8383	1815
166974	0.8127	449

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	97.83	gold quality
mucosa of transverse colon	UBERON:0004991	97.48	gold quality
kidney epithelium	UBERON:0004819	97.46	gold quality
apex of heart	UBERON:0002098	97.38	gold quality
islet of Langerhans	UBERON:0000006	97.14	gold quality
rectum	UBERON:0001052	97.05	gold quality
tibialis anterior	UBERON:0001385	97.05	gold quality
right adrenal gland	UBERON:0001233	97.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.97	gold quality
cardiac muscle of right atrium	UBERON:0003379	96.91	gold quality
upper arm skin	UBERON:0004263	96.90	gold quality
right adrenal gland cortex	UBERON:0035827	96.85	gold quality
left adrenal gland	UBERON:0001234	96.73	gold quality
body of stomach	UBERON:0001161	96.67	gold quality
gastrocnemius	UBERON:0001388	96.63	gold quality
left adrenal gland cortex	UBERON:0035825	96.59	gold quality
muscle of leg	UBERON:0001383	96.40	gold quality
ileal mucosa	UBERON:0000331	96.33	gold quality
myocardium	UBERON:0002349	96.29	gold quality
adrenal cortex	UBERON:0001235	96.25	gold quality
heart left ventricle	UBERON:0002084	96.25	gold quality
skeletal muscle organ	UBERON:0014892	96.25	gold quality
cardiac ventricle	UBERON:0002082	96.13	gold quality
prefrontal cortex	UBERON:0000451	96.09	gold quality
adrenal gland	UBERON:0002369	96.05	gold quality
muscle tissue	UBERON:0002385	96.05	gold quality
right atrium auricular region	UBERON:0006631	96.05	gold quality
cardiac atrium	UBERON:0002081	96.01	gold quality
hypothalamus	UBERON:0001898	96.00	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting MRPL27, 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-150-5P	99.99	66.69	1976
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-7977	98.65	66.18	2590

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 81.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• MRPL27 contributes to unfavorable overall survival and disease-free survival from cholangiocarcinoma patients. (PMID:33456351)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mrpl27	ENSDARG00000032985
mus_musculus	Mrpl27	ENSMUSG00000024414
rattus_norvegicus	Mrpl27	ENSRNOG00000003724

Protein

Protein identifiers

Large ribosomal subunit protein bL27m — Q9P0M9 (reviewed: Q9P0M9)

Alternative names: 39S ribosomal protein L27, mitochondrial

All UniProt accessions (5): Q9P0M9, B3KN43, D6RAN8, D6RE11, H7C5U8

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Component of the mitochondrial large ribosomal subunit (mt-LSU). Mature mammalian 55S mitochondrial ribosomes consist of a small (28S) and a large (39S) subunit. The 28S small subunit contains a 12S ribosomal RNA (12S mt-rRNA) and 30 different proteins. The 39S large subunit contains a 16S rRNA (16S mt-rRNA), a copy of mitochondrial valine transfer RNA (mt-tRNA(Val)), which plays an integral structural role, and 52 different proteins.

Subcellular location. Mitochondrion.

Similarity. Belongs to the bacterial ribosomal protein bL27 family.

RefSeq proteins (1): NP_057588* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001684	Ribosomal_bL27	Family

Pfam: PF01016

UniProt features (13 total): strand 9, transit peptide 1, chain 1, sequence variant 1, helix 1

Structure

Experimental structures (PDB)

87 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
7OF0	ELECTRON MICROSCOPY	2.2
7QI4	ELECTRON MICROSCOPY	2.21
8RRI	ELECTRON MICROSCOPY	2.4
8QU5	ELECTRON MICROSCOPY	2.42
9OLF	ELECTRON MICROSCOPY	2.46
7OF7	ELECTRON MICROSCOPY	2.5
7PO4	ELECTRON MICROSCOPY	2.56
6ZM6	ELECTRON MICROSCOPY	2.59
7O9M	ELECTRON MICROSCOPY	2.6
7OF6	ELECTRON MICROSCOPY	2.6
9CN3	ELECTRON MICROSCOPY	2.62
7QI5	ELECTRON MICROSCOPY	2.63
7OF2	ELECTRON MICROSCOPY	2.7
7OF3	ELECTRON MICROSCOPY	2.7
7OF4	ELECTRON MICROSCOPY	2.7
8QU1	ELECTRON MICROSCOPY	2.74
9PR4	ELECTRON MICROSCOPY	2.77
9PRA	ELECTRON MICROSCOPY	2.83
8ANY	ELECTRON MICROSCOPY	2.85
6ZM5	ELECTRON MICROSCOPY	2.89
7QH7	ELECTRON MICROSCOPY	2.89
7ODR	ELECTRON MICROSCOPY	2.9
7OF5	ELECTRON MICROSCOPY	2.9
8K2A	ELECTRON MICROSCOPY	2.9
8OIT	ELECTRON MICROSCOPY	2.9
9PGL	ELECTRON MICROSCOPY	2.9
9PGF	ELECTRON MICROSCOPY	2.93
6VMI	ELECTRON MICROSCOPY	2.96
6VLZ	ELECTRON MICROSCOPY	2.97
7QI6	ELECTRON MICROSCOPY	2.98

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P0M9-F1	87.52	0.72

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-5368286	Mitochondrial translation initiation
R-HSA-5389840	Mitochondrial translation elongation
R-HSA-5419276	Mitochondrial translation termination
R-HSA-9937383	Mitochondrial ribosome-associated quality control
R-HSA-392499	Metabolism of proteins
R-HSA-5368287	Mitochondrial translation
R-HSA-72766	Translation

MSigDB gene sets: 177 (showing top): MODULE_255, RORA1_01, GOBP_MITOCHONDRIAL_TRANSLATION, MODULE_317, GOBP_TRANSLATION, WEI_MYCN_TARGETS_WITH_E_BOX, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, USF_01, KONDO_COLON_CANCER_HCP_WITH_H3K27ME1, GOCC_MITOCHONDRIAL_ENVELOPE, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, USF_02, WONG_MITOCHONDRIA_GENE_MODULE, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOCC_LARGE_RIBOSOMAL_SUBUNIT

GO Biological Process (2): translation (GO:0006412), mitochondrial translation (GO:0032543)

GO Molecular Function (3): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), protein binding (GO:0005515)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial large ribosomal subunit (GO:0005762), ribosome (GO:0005840), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Mitochondrial translation	4
Translation	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
peptidyltransferase activity	1
translational initiation	1
translational elongation	1
translational termination	1
macromolecule biosynthetic process	1
protein metabolic process	1
protein biosynthetic process	1
mitochondrion	1
translation	1
mitochondrial gene expression	1
nucleic acid binding	1
structural molecule activity	1
ribosome	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
organellar large ribosomal subunit	1
mitochondrial ribosome	1
mitochondrial protein-containing complex	1
intracellular membraneless organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

3159 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MRPL27	RPL26L1	Q9UNX3	573
MRPL27	DPP10	Q8N608	507
MRPL27	DPP6	P42658	478
MRPL27	IMPA1	P29218	453
MRPL27	RPS16	P17008	449
MRPL27	GPR139	Q6DWJ6	392
MRPL27	MTFMT	Q96DP5	353
MRPL27	MRPL32	Q9BYC8	353
MRPL27	METTL15	A6NJ78	353
MRPL27	MRPL33	O75394	353
MRPL27	RPS11	P04643	353
MRPL27	RPS15	P11174	353
MRPL27	RPL23	P23131	353
MRPL27	RPS3	P23396	353
MRPL27	RPL11	P25121	353
MRPL27	RPS18	P25232	353
MRPL27	RPL23A	P29316	353
MRPL27	RPL35	P42766	353
MRPL27	RPL5	P46777	353
MRPL27	MRPL19	P49406	353
MRPL27	TUFM	P49411	353
MRPL27	MRPL12	P52815	353
MRPL27	ALDH18A1	P54886	353
MRPL27	MRPS6	P82932	353

IntAct

101 interactions, top by confidence:

A	B	Type	Score
YBX1	HNRNPR	psi-mi:“MI:0914”(association)	0.770
KBTBD7	METTL15	psi-mi:“MI:0914”(association)	0.730
MRPL27	FHL3	psi-mi:“MI:0915”(physical association)	0.720
FHL3	MRPL27	psi-mi:“MI:0915”(physical association)	0.720
MRPL37	HSPD1	psi-mi:“MI:0914”(association)	0.710
MRPS30	GTPBP10	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NP	KPNA6	psi-mi:“MI:0914”(association)	0.550
RPS6	IPO7	psi-mi:“MI:0914”(association)	0.530
MRPL50	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPL18	NOP56	psi-mi:“MI:0914”(association)	0.530
MRPL10	ZZEF1	psi-mi:“MI:0914”(association)	0.530
RPL7	ZBTB24	psi-mi:“MI:0914”(association)	0.530
MRPL42	GATC	psi-mi:“MI:0914”(association)	0.530
PDGFB	DKC1	psi-mi:“MI:0914”(association)	0.530
MRPL28	MRPL3	psi-mi:“MI:0914”(association)	0.530
MRPL41	MRPL3	psi-mi:“MI:0914”(association)	0.530
YBX1	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
THAP3	CASC3	psi-mi:“MI:0914”(association)	0.530
MRPL27	MRPL33	psi-mi:“MI:0914”(association)	0.530
NDUFAB1	MIEF1	psi-mi:“MI:0915”(physical association)	0.490
MRPL27		psi-mi:“MI:0915”(physical association)	0.370
FOXB1	DDX39A	psi-mi:“MI:0914”(association)	0.350
ALYREF		psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
MRPL4	ZSWIM8	psi-mi:“MI:0914”(association)	0.350

BioGRID (283): MRPL27 (Two-hybrid), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL27 (Affinity Capture-MS)

ESM2 similar proteins: A0A2Z5WA18, A0A4P8DJE6, A2YQ56, B5X2B8, B5XAM2, B9FK36, C0HKA0, C0HKA1, G1T1F0, O60086, P10735, P13471, P15126, P34378, P38120, P42847, P48150, P54889, P62263, P62264, P62265, P82195, P82911, P82912, Q04599, Q08699, Q1K699, Q3ZBR7, Q59HJ6, Q5UAM9, Q69UZ3, Q6AVG6, Q6CJ65, Q6FL25, Q6XI08, Q754Q9, Q757I0, Q75DV9, Q7KUT2, Q7RZF0

Diamond homologs: A0LCZ4, A0LPF8, A1KAC9, A1URM7, A4YKF6, A5CF98, A5E968, A5F8P1, A5VSI8, A6UDV3, A6WXR7, A7HT69, A7IH94, A8EZV2, A8F2N7, A8GPP8, A8GTK7, A8GYB3, A8HRT6, A9IM57, A9M886, A9VYM7, A9WWX2, B0BV44, B0T395, B0UMS2, B1M699, B1XT34, B1ZL17, B2IE46, B2S810, B3CV08, B3EUD7, B3PRY9, B3Q726, B4RZH4, B5ELU3, B5FGF8, B5YJ66, B5ZUD9

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
MRPL27	“form complex”	“39S mitochondrial large ribosomal subunit”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 106 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
Mitochondrial ribosome-associated quality control	25	39.4×	1e-31
Mitochondrial translation initiation	23	37.4×	1e-28
Mitochondrial translation elongation	23	37.4×	1e-28
Mitochondrial translation	21	37.0×	4e-26
Mitochondrial translation termination	23	32.4×	3e-27
Translation	24	19.1×	8e-23
Peptide chain elongation	7	11.4×	1e-04
Viral mRNA Translation	7	11.4×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
mitochondrial translation	25	44.3×	2e-32
translation	20	21.0×	9e-19
cytoplasmic translation	7	13.2×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

791 predictions. Top by Δscore:

Variant	Effect	Δscore
17:50370450:CTCA:C	donor_loss	1.0000
17:50370451:TCA:T	donor_loss	1.0000
17:50370452:CA:C	donor_loss	1.0000
17:50370453:ACC:A	donor_loss	1.0000
17:50370457:T:A	donor_gain	1.0000
17:50370468:AATG:A	donor_gain	1.0000
17:50370582:TGTAA:T	acceptor_gain	1.0000
17:50370583:GTAA:G	acceptor_gain	1.0000
17:50370584:TAA:T	acceptor_gain	1.0000
17:50370585:AA:A	acceptor_gain	1.0000
17:50370587:C:CC	acceptor_gain	1.0000
17:50373130:CCGG:C	donor_gain	1.0000
17:50370030:A:AC	donor_gain	0.9900
17:50370031:C:CC	donor_gain	0.9900
17:50370308:T:TA	donor_gain	0.9900
17:50370449:CCTCA:C	donor_loss	0.9900
17:50370453:A:AC	donor_gain	0.9900
17:50370453:ACCTT:A	donor_gain	0.9900
17:50370454:C:CC	donor_gain	0.9900
17:50370454:CCTT:C	donor_gain	0.9900
17:50370454:CCTTC:C	donor_gain	0.9900
17:50370494:TTCC:T	donor_gain	0.9900
17:50370590:C:CT	acceptor_gain	0.9900
17:50370591:A:T	acceptor_gain	0.9900
17:50373114:C:CT	donor_gain	0.9900
17:50373115:T:TT	donor_gain	0.9900
17:50373122:T:TA	donor_gain	0.9900
17:50373123:C:A	donor_gain	0.9900
17:50373127:TTAC:T	donor_loss	0.9900
17:50373128:TACCG:T	donor_loss	0.9900

AlphaMissense

937 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:50368249:A:T	V97D	0.994
17:50368147:A:T	V131D	0.992
17:50368149:A:C	F130L	0.992
17:50368149:A:T	F130L	0.992
17:50368151:A:G	F130L	0.992
17:50370090:A:T	V61D	0.989
17:50368113:G:C	F142L	0.986
17:50368113:G:T	F142L	0.986
17:50368115:A:G	F142L	0.986
17:50368267:G:T	A91D	0.985
17:50370072:A:T	I67N	0.985
17:50368256:C:A	G95W	0.984
17:50368256:C:G	G95R	0.983
17:50368256:C:T	G95R	0.983
17:50368155:C:A	K128N	0.981
17:50368155:C:G	K128N	0.981
17:50368255:C:A	G95V	0.980
17:50368255:C:T	G95E	0.979
17:50370072:A:C	I67S	0.975
17:50368141:A:T	V133E	0.971
17:50368297:A:T	V81E	0.970
17:50370081:C:A	G64V	0.970
17:50370049:A:G	W75R	0.969
17:50370049:A:T	W75R	0.969
17:50370069:G:T	A68E	0.969
17:50370528:C:A	K33N	0.968
17:50370528:C:G	K33N	0.968
17:50368246:C:G	R98P	0.967
17:50370039:C:T	G78D	0.959
17:50370039:C:A	G78V	0.958

dbSNP variants (sampled 300 via entrez): RS1000212586 (17:50374678 C>A,G,T), RS1000622582 (17:50374853 AAAG>A), RS1000804350 (17:50367662 G>C), RS1001373544 (17:50369865 T>C), RS1001835083 (17:50374427 C>T), RS1001985952 (17:50368026 G>A), RS1002130400 (17:50373177 G>A,T), RS1002619509 (17:50371789 A>G), RS1003889449 (17:50374296 C>T), RS1004261224 (17:50374083 G>C), RS1005285664 (17:50373984 C>G,T), RS1005524654 (17:50372816 T>C,G), RS1005971661 (17:50372986 A>G,T), RS1006272685 (17:50371332 C>G), RS1007369850 (17:50371040 T>C)

Disease associations

OMIM: gene MIM:611837 | 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)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Acetaminophen	affects expression, decreases expression	2
Progesterone	affects cotreatment, decreases expression	2
dicrotophos	decreases expression	1
bisphenol A	affects cotreatment, decreases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Dimethyl Sulfoxide	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ribonucleotides	affects binding	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Aflatoxin B1	increases methylation	1
Asbestos, Crocidolite	increases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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