MALSU1

Summary

MALSU1 (mitochondrial assembly of ribosomal large subunit 1, HGNC:21721) is a protein-coding gene on chromosome 7p15.3, encoding Mitochondrial assembly of ribosomal large subunit protein 1 (Q96EH3). Required for normal mitochondrial ribosome function and mitochondrial translation.

Enables mitochondrial large ribosomal subunit binding activity. Involved in negative regulation of mitochondrial translation and ribosomal large subunit biogenesis. Located in cytosol and mitochondrion.

Source: NCBI Gene 115416 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_138446

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21721
Approved symbol	MALSU1
Name	mitochondrial assembly of ribosomal large subunit 1
Location	7p15.3
Locus type	gene with protein product
Status	Approved
Aliases	mtRsfA
Ensembl gene	ENSG00000156928
Ensembl biotype	protein_coding
OMIM	614624
Entrez	115416

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 retained_intron, 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000287543, ENST00000466681, ENST00000476623, ENST00000479974, ENST00000481564, ENST00000924618, ENST00000956356

RefSeq mRNA: 1 — MANE Select: NM_138446 NM_138446

CCDS: CCDS5381

Canonical transcript exons

ENST00000466681 — 4 exons

Exon	Start	End
ENSE00001029125	23307868	23307949
ENSE00001914967	23299339	23299608
ENSE00001927791	23309356	23311729
ENSE00003656105	23300839	23301017

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 68.4743 / max 266.6193, expressed in 1822 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77664	68.4743	1822

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.87	gold quality
epithelial cell of pancreas	CL:0000083	99.64	gold quality
left ventricle myocardium	UBERON:0006566	99.48	gold quality
cardiac muscle of right atrium	UBERON:0003379	99.10	gold quality
deltoid	UBERON:0001476	99.06	gold quality
pigmented layer of retina	UBERON:0001782	99.00	gold quality
vastus lateralis	UBERON:0001379	98.97	gold quality
myocardium	UBERON:0002349	98.92	gold quality
quadriceps femoris	UBERON:0001377	98.91	gold quality
tibialis anterior	UBERON:0001385	98.91	gold quality
pancreatic ductal cell	CL:0002079	98.83	gold quality
germinal epithelium of ovary	UBERON:0001304	98.76	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	98.59	gold quality
tibia	UBERON:0000979	98.58	gold quality
gingival epithelium	UBERON:0001949	98.50	gold quality
esophagus squamous epithelium	UBERON:0006920	98.38	gold quality
parietal pleura	UBERON:0002400	98.36	gold quality
palpebral conjunctiva	UBERON:0001812	98.35	gold quality
biceps brachii	UBERON:0001507	98.33	gold quality
kidney epithelium	UBERON:0004819	98.33	gold quality
body of tongue	UBERON:0011876	98.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	98.27	gold quality
visceral pleura	UBERON:0002401	98.25	gold quality
heart right ventricle	UBERON:0002080	98.11	gold quality
skeletal muscle tissue	UBERON:0001134	97.94	gold quality
upper arm skin	UBERON:0004263	97.92	gold quality
tongue	UBERON:0001723	97.75	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.65	gold quality
gingiva	UBERON:0001828	97.64	gold quality
renal medulla	UBERON:0000362	97.57	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

Literature-anchored findings (GeneRIF, showing 3)

• C7orf30 is proposed to be involved in ribosomal large subunit function. (PMID:22238375)
• C7orf30 is a novel human gene indispensable for mitochondrial translation, most probably via its contribution to the biogenesis of the large subunit of the mitochondrial ribosome. (PMID:22238376)
• C7orf30 promotes incorporation of MRPL14 into the mitochondrial large ribosomal subunit. (PMID:23171548)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	malsu1	ENSDARG00000091079
mus_musculus	Malsu1	ENSMUSG00000029815
rattus_norvegicus	Malsu1	ENSRNOG00000009035
drosophila_melanogaster	CG9166	FBGN0029514

Protein

Protein identifiers

Mitochondrial assembly of ribosomal large subunit protein 1 — Q96EH3 (reviewed: Q96EH3)

All UniProt accessions (1): Q96EH3

UniProt curated annotations — full annotation on UniProt →

Function. Required for normal mitochondrial ribosome function and mitochondrial translation. May play a role in ribosome biogenesis by preventing premature association of the 28S and 39S ribosomal subunits. Interacts with mitochondrial ribosomal protein uL14m (MRPL14), probably blocking formation of intersubunit bridge B8, preventing association of the 28S and 39S ribosomal subunits. Addition to isolated mitochondrial ribosomal subunits partially inhibits translation, probably by interfering with the association of the 28S and 39S ribosomal subunits and the formation of functional ribosomes. May also participate in the assembly and/or regulation of the stability of the large subunit of the mitochondrial ribosome. May function as a ribosomal silencing factor.

Subunit / interactions. Associates with the mitochondrial ribosome large subunit (39S) via interaction with MRPL12 and/or MRPL14. The interaction generates steric hindrance that is expected to prevent premature association of the 28S and 39S ribosomal subunits. Interacts with intermediates of the mitochondrial ribosome large subunit (mt-LSU) (recruits the mitochondrial ribosome and complex I assembly factor AltMIEF1 and NDUFAB1); regulates mitochondrial ribosomes assembly. Interacts with MRPL12 and MRPL14.

Subcellular location. Mitochondrion matrix.

Similarity. Belongs to the Iojap/RsfS family.

RefSeq proteins (1): NP_612455* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004394	Iojap/RsfS/C7orf30	Family
IPR043519	NT_sf	Homologous_superfamily

Pfam: PF02410

UniProt features (13 total): strand 7, helix 4, chain 1, region of interest 1

Structure

Experimental structures (PDB)

30 structures.

PDB	Method	Resolution (Å)
7OF0	ELECTRON MICROSCOPY	2.2
8QU5	ELECTRON MICROSCOPY	2.42
7OF7	ELECTRON MICROSCOPY	2.5
7PO4	ELECTRON MICROSCOPY	2.56
7O9M	ELECTRON MICROSCOPY	2.6
7OF2	ELECTRON MICROSCOPY	2.7
7OF3	ELECTRON MICROSCOPY	2.7
9PRA	ELECTRON MICROSCOPY	2.83
7QH7	ELECTRON MICROSCOPY	2.89
7ODR	ELECTRON MICROSCOPY	2.9
7OF5	ELECTRON MICROSCOPY	2.9
8QSJ	ELECTRON MICROSCOPY	3
5OOM	ELECTRON MICROSCOPY	3.03
8PK0	ELECTRON MICROSCOPY	3.03
5OOL	ELECTRON MICROSCOPY	3.06
7QH6	ELECTRON MICROSCOPY	3.08
7A5J	ELECTRON MICROSCOPY	3.1
7O9K	ELECTRON MICROSCOPY	3.1
7ODS	ELECTRON MICROSCOPY	3.1
7ODT	ELECTRON MICROSCOPY	3.1
7OIC	ELECTRON MICROSCOPY	3.1
7A5H	ELECTRON MICROSCOPY	3.3
7OI9	ELECTRON MICROSCOPY	3.3
7PD3	ELECTRON MICROSCOPY	3.4
8K2B	ELECTRON MICROSCOPY	3.4
7OI7	ELECTRON MICROSCOPY	3.5
7OI8	ELECTRON MICROSCOPY	3.5
7OIE	ELECTRON MICROSCOPY	3.5
7OID	ELECTRON MICROSCOPY	3.7
7OI6	ELECTRON MICROSCOPY	5.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EH3-F1	70.73	0.43

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9937383	Mitochondrial ribosome-associated quality control

MSigDB gene sets: 96 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GOBP_RIBOSOME_BIOGENESIS, GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_RIBOSOME_ASSEMBLY, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, PATIL_LIVER_CANCER, GOBP_TRANSLATION, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN

GO Biological Process (6): negative regulation of translation (GO:0017148), ribosomal large subunit biogenesis (GO:0042273), negative regulation of mitochondrial translation (GO:0070130), negative regulation of ribosome biogenesis (GO:0090071), mitochondrial large ribosomal subunit assembly (GO:1902775), ribosome biogenesis (GO:0042254)

GO Molecular Function (3): ribosomal large subunit binding (GO:0043023), mitochondrial large ribosomal subunit binding (GO:0140978), protein binding (GO:0005515)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Mitochondrial translation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribonucleoprotein complex biogenesis	2
ribosome biogenesis	2
cytoplasm	2
translation	1
regulation of translation	1
negative regulation of gene expression	1
negative regulation of protein metabolic process	1
negative regulation of translation	1
mitochondrial translation	1
regulation of mitochondrial translation	1
negative regulation of cellular process	1
regulation of ribosome biogenesis	1
ribosomal large subunit assembly	1
mitochondrial ribosome assembly	1
ribosome binding	1
ribosomal large subunit binding	1
mitochondrial ribosome binding	1
binding	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1804 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MALSU1	MTG1	Q9BT17	866
MALSU1	MTG2	Q9H4K7	844
MALSU1	NSUN4	Q96CB9	840
MALSU1	GTPBP10	A4D1E9	835
MALSU1	MTERF4	Q7Z6M4	829
MALSU1	GTPBP6	O43824	769
MALSU1	MRM3	Q9HC36	761
MALSU1	DDX28	Q9NUL7	731
MALSU1	MRM2	Q9UI43	711
MALSU1	MTERF3	Q96E29	703
MALSU1	RPUSD4	Q96CM3	658
MALSU1	NOA1	Q8NC60	653
MALSU1	MRPL58	Q14197	643
MALSU1	MTIF2	P46199	635
MALSU1	ERAL1	O75616	633
MALSU1	PTCD1	O75127	633

IntAct

172 interactions, top by confidence:

A	B	Type	Score
DCTD	MALSU1	psi-mi:“MI:0915”(physical association)	0.720
MALSU1	DCTD	psi-mi:“MI:0915”(physical association)	0.720
MRPL37	HSPD1	psi-mi:“MI:0914”(association)	0.710
MALSU1	NDUFAB1	psi-mi:“MI:0914”(association)	0.710
MRPS30	GTPBP10	psi-mi:“MI:0914”(association)	0.640
PLEKHG4	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
MALSU1	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
LMO3	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
INCA1	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
MALSU1	ZNF426	psi-mi:“MI:0915”(physical association)	0.560
MYBPHL	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
ZFP90	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
SP6	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
MALSU1		psi-mi:“MI:0915”(physical association)	0.560
HTT	MALSU1	psi-mi:“MI:0915”(physical association)	0.560
MRPL50	GTPBP10	psi-mi:“MI:0914”(association)	0.530
CIRBP	PRMT5	psi-mi:“MI:0914”(association)	0.530
MRPL10	ZZEF1	psi-mi:“MI:0914”(association)	0.530

BioGRID (221): MALSU1 (Two-hybrid), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS), MALSU1 (Affinity Capture-MS)

ESM2 similar proteins: A6H773, A6QPI4, B1AR13, E1BH29, O48965, O75208, O75380, P22682, P30291, P47810, P56726, P82670, P97698, Q08BI9, Q0MQH5, Q0MQH6, Q0MQH7, Q12849, Q2NL34, Q2T9V7, Q39471, Q39664, Q496Y0, Q4R5X8, Q5C9Z4, Q5M8Z2, Q5T6X4, Q5U1Z8, Q5VUE5, Q5XIU9, Q5ZLJ4, Q63802, Q66JB6, Q6DVA0, Q6ZWB6, Q78JW9, Q7Z7K6, Q80UU9, Q8C5Q4, Q8HXH0

Diamond homologs: O83720, Q02SH2, Q96EH3, P0AAT6, P0AAT7, P0AAT8, P44471, P54457, P73658, Q5NLX3, Q7P0P8, Q97P97, Q9CAF9, Q9CWV0, Q9KD89, P34523, Q41822, Q9LDY9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 128 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	34	45.4×	3e-47
Mitochondrial translation initiation	32	44.1×	3e-44
Mitochondrial translation elongation	32	44.1×	3e-44
Mitochondrial translation	29	43.4×	1e-39
Mitochondrial translation termination	32	38.2×	6e-42
Translation	30	20.2×	4e-30

GO biological processes:

GO term	Partners	Fold	FDR
mitochondrial large ribosomal subunit assembly	6	48.8×	3e-07
mitochondrial translation	33	47.0×	7e-45
translation	23	19.4×	6e-21
RNA processing	6	10.8×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

669 predictions. Top by Δscore:

Variant	Effect	Δscore
7:23299606:C:T	donor_gain	0.9900
7:23307866:A:AG	acceptor_gain	0.9900
7:23307867:G:GG	acceptor_gain	0.9900
7:23309354:A:AG	acceptor_gain	0.9900
7:23309355:G:GG	acceptor_gain	0.9900
7:23299312:G:GT	donor_gain	0.9800
7:23299606:CAGGT:C	donor_loss	0.9800
7:23299607:AGGTA:A	donor_loss	0.9800
7:23299608:GGTAC:G	donor_loss	0.9800
7:23299609:G:GA	donor_loss	0.9800
7:23299610:T:A	donor_loss	0.9800
7:23309355:GGCA:G	acceptor_gain	0.9800
7:23301016:TGGT:T	donor_loss	0.9700
7:23301019:T:G	donor_loss	0.9700
7:23307867:GTACA:G	acceptor_gain	0.9700
7:23309351:GACA:G	acceptor_loss	0.9600
7:23309352:ACAG:A	acceptor_loss	0.9600
7:23309353:CA:C	acceptor_loss	0.9600
7:23307867:GTAC:G	acceptor_gain	0.9500
7:23309344:T:A	acceptor_loss	0.9500
7:23299801:C:T	donor_gain	0.9400
7:23300838:GATC:G	acceptor_gain	0.9400
7:23309350:T:TA	acceptor_gain	0.9400
7:23301018:G:GG	donor_gain	0.9300
7:23299833:G:GT	donor_gain	0.9200
7:23301020:A:C	donor_loss	0.9200
7:23309355:GGC:G	acceptor_gain	0.9200
7:23299757:T:TA	donor_gain	0.9100
7:23300830:GCATT:G	acceptor_loss	0.9100
7:23300832:ATTTC:A	acceptor_loss	0.9100

AlphaMissense

1516 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:23309418:T:A	W194R	0.997
7:23309418:T:C	W194R	0.997
7:23307931:T:A	W167R	0.996
7:23307931:T:C	W167R	0.996
7:23307939:C:G	C169W	0.996
7:23309393:A:C	R185S	0.996
7:23309393:A:T	R185S	0.996
7:23300968:G:A	G129E	0.995
7:23309392:G:T	R185I	0.995
7:23309407:T:C	L190S	0.995
7:23309410:A:T	E191V	0.995
7:23309420:G:C	W194C	0.995
7:23309420:G:T	W194C	0.995
7:23307933:G:C	W167C	0.994
7:23307933:G:T	W167C	0.994
7:23309370:C:G	H178D	0.994
7:23309392:G:C	R185T	0.994
7:23307938:G:A	C169Y	0.992
7:23300973:T:C	S131P	0.991
7:23300899:C:A	A106E	0.990
7:23307937:T:C	C169R	0.990
7:23309416:T:C	L193S	0.990
7:23300982:C:G	H134D	0.988
7:23300991:G:C	A137P	0.988
7:23309419:G:C	W194S	0.988
7:23300964:A:C	S128R	0.987
7:23300966:T:A	S128R	0.987
7:23300966:T:G	S128R	0.987
7:23307935:T:C	L168P	0.987
7:23309410:A:C	E191A	0.987

dbSNP variants (sampled 300 via entrez): RS1000045299 (7:23297582 G>A,T), RS1000358379 (7:23307740 G>A,C,T), RS1000740361 (7:23298239 A>G), RS1000829680 (7:23301881 A>G), RS1001483215 (7:23303756 C>T), RS1001503465 (7:23297962 C>T), RS1001703010 (7:23297721 G>A), RS1001997291 (7:23300212 G>A), RS1002100999 (7:23302999 A>G), RS1002484437 (7:23305126 T>C), RS1002704384 (7:23299067 C>A,G,T), RS1002747443 (7:23299989 A>T), RS1002910221 (7:23309158 C>T), RS1002928522 (7:23303679 G>A,T), RS1002937082 (7:23301269 T>C)

Disease associations

OMIM: gene MIM:614624 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Leflunomide	decreases expression	2
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
K 7174	decreases expression	1
abrine	decreases expression	1
bisphenol S	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Copper	increases expression, affects cotreatment	1
Diethylstilbestrol	affects expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ketoconazole	increases expression	1
Methyl Methanesulfonate	decreases expression	1
Quercetin	decreases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Cyclosporine	decreases 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.