CMSS1

Summary

CMSS1 (cms1 ribosomal small subunit homolog, HGNC:28666) is a protein-coding gene on chromosome 3q12.1, encoding Protein CMSS1 (Q9BQ75).

Enables RNA binding activity.

Source: NCBI Gene 84319 — RefSeq curated summary.

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 238 total
• MANE Select transcript: NM_032359

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28666
Approved symbol	CMSS1
Name	cms1 ribosomal small subunit homolog
Location	3q12.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC4308
Ensembl gene	ENSG00000184220
Ensembl biotype	protein_coding
Entrez	84319

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000421999, ENST00000463526, ENST00000478909, ENST00000479555, ENST00000489081, ENST00000491299, ENST00000494412, ENST00000496116, ENST00000497345

RefSeq mRNA: 2 — MANE Select: NM_032359 NM_001167924, NM_032359

CCDS: CCDS2935, CCDS54618

Canonical transcript exons

ENST00000421999 — 10 exons

Exon	Start	End
ENSE00001307208	100176327	100176415
ENSE00001329180	100172316	100172403
ENSE00001919600	99817862	99818043
ENSE00002611074	100178305	100181732
ENSE00003467608	100166335	100166394
ENSE00003495102	100146973	100147061
ENSE00003496678	100160430	100160501
ENSE00003540674	100167738	100167840
ENSE00003670373	100162303	100162432
ENSE00003678255	100171839	100171899

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 96.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 52.8010 / max 587.1923, expressed in 1815 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
37583	27.0416	1795
37584	18.5749	1756
37582	7.0819	1577
37594	0.1027	32

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	96.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.94	gold quality
prefrontal cortex	UBERON:0000451	93.66	gold quality
endothelial cell	CL:0000115	93.45	gold quality
popliteal artery	UBERON:0002250	93.40	gold quality
tibial artery	UBERON:0007610	93.39	gold quality
cortical plate	UBERON:0005343	93.05	gold quality
gastrocnemius	UBERON:0001388	93.00	gold quality
ganglionic eminence	UBERON:0004023	93.00	gold quality
calcaneal tendon	UBERON:0003701	92.77	gold quality
ventricular zone	UBERON:0003053	92.73	gold quality
aorta	UBERON:0000947	92.59	gold quality
anterior cingulate cortex	UBERON:0009835	92.55	gold quality
muscle of leg	UBERON:0001383	92.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.32	gold quality
left coronary artery	UBERON:0001626	92.18	gold quality
hypothalamus	UBERON:0001898	92.16	gold quality
body of pancreas	UBERON:0001150	92.07	gold quality
left adrenal gland cortex	UBERON:0035825	92.05	gold quality
right frontal lobe	UBERON:0002810	91.79	gold quality
left adrenal gland	UBERON:0001234	91.78	gold quality
ascending aorta	UBERON:0001496	91.78	gold quality
thoracic aorta	UBERON:0001515	91.73	gold quality
right testis	UBERON:0004534	91.73	gold quality
cerebellar cortex	UBERON:0002129	91.68	gold quality
neocortex	UBERON:0001950	91.64	gold quality
cerebellar hemisphere	UBERON:0002245	91.64	gold quality
frontal cortex	UBERON:0001870	91.62	gold quality
left testis	UBERON:0004533	91.60	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.59	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	10.89
E-CURD-112	yes	8.17
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CMSS1, 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-4795-3P	100.00	74.62	4024
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-106A-3P	99.53	67.58	995
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-6755-3P	98.61	66.90	834
HSA-MIR-628-5P	98.36	67.74	844
HSA-MIR-1267	98.24	69.05	837
HSA-MIR-4327	97.21	67.71	676
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-759	96.16	66.77	873

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cmss1	ENSDARG00000112579
mus_musculus	Cmss1	ENSMUSG00000022748
rattus_norvegicus	Cmss1	ENSRNOG00000027888

Protein

Protein identifiers

Protein CMSS1 — Q9BQ75 (reviewed: Q9BQ75)

Alternative names: Cms1 ribosomal small subunit homolog

All UniProt accessions (5): C9IY68, C9J384, Q9BQ75, F8WC72, H7C515

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CMS1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BQ75-1	1	yes
Q9BQ75-2	2

RefSeq proteins (2): NP_001161396, NP_115735* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR032704	Cms1	Family

Pfam: PF14617

UniProt features (13 total): modified residue 4, sequence variant 2, sequence conflict 2, compositionally biased region 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQ75-F1	80.31	0.62

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 (4): 19, 24, 167, 212

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 146 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, ATF_B, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, ATGTTAA_MIR302C, CREB_Q4, WEI_MYCN_TARGETS_WITH_E_BOX, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, ATF3_Q6, CREB_Q2_01, ATF4_Q2, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CREB_Q3, FISCHER_DREAM_TARGETS, ACEVEDO_LIVER_CANCER_UP, ATF_01

GO Biological Process (0):

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
binding	1

Protein interactions and networks

STRING

1602 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CMSS1	ZC3H11B	A0A1B0GTU1	734
CMSS1	GJD2	Q9UKL4	505
CMSS1	ZNRF3	Q9ULT6	477
CMSS1	ALPG	P10696	476
CMSS1	DEDD2	Q8WXF8	455
CMSS1	R3HDM4	Q96D70	437
CMSS1	FILIP1L	Q4L180	435
CMSS1	RSPO1	Q2MKA7	420
CMSS1	LAMA2	P24043	420
CMSS1	ATF7IP	Q6VMQ6	403
CMSS1	MGARP	Q8TDB4	379
CMSS1	C16orf90	A8MZG2	375
CMSS1	PSME3IP1	Q9GZU8	351
CMSS1	MPP4	Q96JB8	351
CMSS1	PSMA6	P34062	349

IntAct

117 interactions, top by confidence:

A	B	Type	Score
CCM2	KRIT1	psi-mi:“MI:0914”(association)	0.960
MED29	MED19	psi-mi:“MI:0914”(association)	0.890
MED17	MED19	psi-mi:“MI:0914”(association)	0.840
SART3	PRPF4	psi-mi:“MI:0914”(association)	0.730
N	HNRNPR	psi-mi:“MI:0914”(association)	0.730
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
PACSIN1	COBLL1	psi-mi:“MI:0914”(association)	0.660
SPANXN3	SUOX	psi-mi:“MI:0914”(association)	0.640
CMSS1	WFS1	psi-mi:“MI:0915”(physical association)	0.560
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
H1-4	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ACSBG2	ZZEF1	psi-mi:“MI:0914”(association)	0.530
PEX19	FAM20B	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
H1-4	RRP8	psi-mi:“MI:0914”(association)	0.530
LUC7L2	ZNF593	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
PBXIP1	KCNN4	psi-mi:“MI:0914”(association)	0.530
CMSS1	HTR6	psi-mi:“MI:0915”(physical association)	0.370
CMSS1	S1PR1	psi-mi:“MI:0915”(physical association)	0.370
GYG1	CMSS1	psi-mi:“MI:0915”(physical association)	0.370
NES	RPL10	psi-mi:“MI:0914”(association)	0.350
FOXI2	DDX39A	psi-mi:“MI:0914”(association)	0.350

BioGRID (159): CMSS1 (Affinity Capture-MS), PCDH7 (Affinity Capture-MS), PSME3 (Affinity Capture-MS), MRGBP (Affinity Capture-MS), MDM2 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS), CMSS1 (Affinity Capture-MS)

ESM2 similar proteins: A5A6J5, D4AB66, E2RSQ2, F1M5F3, F1N2W9, F1QDI9, I0IUP4, O14795, P17863, P22681, P22682, P49797, Q02040, Q15014, Q24K03, Q2KHI9, Q2KJ58, Q2T9Y1, Q2YDJ8, Q496Y0, Q4KUS2, Q4R578, Q52L14, Q56K12, Q5C9Z4, Q5F3L9, Q5M7C8, Q5R6Y9, Q5R905, Q62768, Q62769, Q66JB6, Q69ZT9, Q6QI89, Q8BND4, Q8BZ60, Q8HXH0, Q8IYS8, Q8N5Y2, Q8VDV3

Diamond homologs: G0S1B3, Q2T9Y1, Q5FVR6, Q5XJK9, Q68EV5, Q9BQ75, Q9CZT6, O94465, A4HRK0, O62591, P0A4D7, P0A4D8, Q25225, O00148, Q5U216, Q8VDW0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 139 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
Eukaryotic Translation Elongation	6	20.1×	7e-05
Eukaryotic Translation Initiation	5	18.6×	2e-04
Cap-dependent Translation Initiation	5	18.6×	2e-04
SARS-CoV-1 modulates host translation machinery	5	18.6×	2e-04
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	5	16.4×	3e-04
SARS-CoV-1-host interactions	7	14.8×	7e-05
Nonsense-Mediated Decay (NMD)	5	14.0×	5e-04
rRNA processing in the nucleus and cytosol	7	13.6×	9e-05

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal small subunit biogenesis	10	17.9×	1e-07
RNA processing	7	12.1×	3e-04
cytoplasmic translation	8	11.7×	1e-04
rRNA processing	8	8.9×	5e-04
translation	10	8.1×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	206
Likely benign	17
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

6320 predictions. Top by Δscore:

Variant	Effect	Δscore
3:100051302:GAGTA:G	donor_gain	1.0000
3:100051304:GTA:G	donor_gain	1.0000
3:100146970:TAG:T	acceptor_loss	1.0000
3:100146971:A:AG	acceptor_gain	1.0000
3:100146972:G:GA	acceptor_gain	1.0000
3:100146972:GA:G	acceptor_gain	1.0000
3:100146972:GAA:G	acceptor_gain	1.0000
3:100146972:GAAGC:G	acceptor_gain	1.0000
3:100147059:CAGG:C	donor_loss	1.0000
3:100147060:AGGT:A	donor_loss	1.0000
3:100147062:G:GA	donor_loss	1.0000
3:100147063:T:A	donor_loss	1.0000
3:100160428:A:AG	acceptor_gain	1.0000
3:100160429:G:GG	acceptor_gain	1.0000
3:100162295:T:G	acceptor_gain	1.0000
3:100162301:A:AG	acceptor_gain	1.0000
3:100162302:G:GG	acceptor_gain	1.0000
3:100162302:GAA:G	acceptor_gain	1.0000
3:100166391:GAAA:G	donor_gain	1.0000
3:100167736:A:AG	acceptor_gain	1.0000
3:100167737:G:GG	acceptor_gain	1.0000
3:100167737:GTT:G	acceptor_gain	1.0000
3:100172304:A:AG	acceptor_gain	1.0000
3:100172304:ATCTT:A	acceptor_gain	1.0000
3:100172305:T:G	acceptor_gain	1.0000
3:100172308:T:A	acceptor_gain	1.0000
3:99986345:CAT:C	acceptor_gain	1.0000
3:99986347:T:TC	acceptor_gain	1.0000
3:100003230:CA:C	acceptor_gain	0.9900
3:100003231:A:C	acceptor_gain	0.9900

AlphaMissense

1829 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:100171882:T:C	F188L	0.985
3:100171884:T:A	F188L	0.985
3:100171884:T:G	F188L	0.985
3:100167749:T:A	W143R	0.984
3:100167749:T:C	W143R	0.984
3:100178383:T:C	F279L	0.983
3:100178385:C:A	F279L	0.983
3:100178385:C:G	F279L	0.983
3:100176368:T:A	W237R	0.979
3:100176368:T:C	W237R	0.979
3:100172368:G:A	G211E	0.973
3:100167834:T:C	L171P	0.971
3:100176360:T:A	V234D	0.971
3:100171852:T:C	F178L	0.969
3:100171854:C:A	F178L	0.969
3:100171854:C:G	F178L	0.969
3:100166386:T:C	L136P	0.968
3:100167808:C:G	C162W	0.967
3:100167751:G:C	W143C	0.965
3:100167751:G:T	W143C	0.965
3:100172367:G:A	G211R	0.962
3:100172367:G:C	G211R	0.962
3:99818004:T:A	W9R	0.962
3:99818004:T:C	W9R	0.962
3:100172392:T:C	L219P	0.961
3:100178384:T:C	F279S	0.961
3:99818006:G:C	W9C	0.961
3:99818006:G:T	W9C	0.961
3:100172362:G:A	G209D	0.960
3:100176373:C:A	N238K	0.959

dbSNP variants (sampled 300 via entrez): RS1000004816 (3:99904708 A>G), RS1000048422 (3:100027567 C>T), RS1000049619 (3:99833364 C>T), RS1000053667 (3:99889444 A>C), RS1000054268 (3:99890725 G>A,T), RS1000075081 (3:100093441 T>A,C), RS1000088533 (3:100120157 A>G), RS1000098534 (3:99944169 C>T), RS1000100568 (3:100175012 C>T), RS1000108258 (3:99882293 T>C), RS1000112198 (3:99988877 T>G), RS1000115249 (3:99897848 T>G), RS1000119093 (3:100140171 A>G), RS1000129984 (3:99944413 C>A,T), RS1000136078 (3:99853285 A>G)

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

20 associations (top):

Study	Trait	p-value
GCST001524_6	Visceral adipose tissue/subcutaneous adipose tissue ratio	7.000000e-06
GCST002115_7	Axial length	5.000000e-11
GCST004988_436	Breast cancer	5.000000e-10
GCST006629_90	Pulse pressure	1.000000e-13
GCST007269_31	Pulse pressure	6.000000e-13
GCST009464_36	Facial morphology	3.000000e-08
GCST010002_434	Refractive error	5.000000e-25
GCST012228_65	Waist-hip index	3.000000e-08
GCST012228_66	Waist-hip index	3.000000e-09
GCST012228_67	Waist-hip index	3.000000e-10
GCST012230_264	Waist-to-hip ratio adjusted for BMI	4.000000e-08
GCST012230_265	Waist-to-hip ratio adjusted for BMI	5.000000e-08
GCST012230_266	Waist-to-hip ratio adjusted for BMI	4.000000e-09
GCST012230_267	Waist-to-hip ratio adjusted for BMI	5.000000e-10
GCST012231_187	A body shape index	1.000000e-08
GCST012231_188	A body shape index	3.000000e-08
GCST90000025_946	Appendicular lean mass	5.000000e-12
GCST90020024_1251	A body shape index	5.000000e-12
GCST90020028_812	Hip circumference adjusted for BMI	3.000000e-09
GCST90020029_1344	Waist circumference adjusted for body mass index	2.000000e-12

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0005318	axial length measurement
EFO:0005763	pulse pressure measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference
EFO:0004980	appendicular lean mass
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression	5
Aflatoxin B1	affects expression, decreases expression, decreases methylation	4
bisphenol A	affects expression, affects cotreatment, affects methylation, increases methylation, increases expression	3
Cyclosporine	decreases methylation, increases expression	3
sodium arsenite	increases abundance, increases expression, decreases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
Cisplatin	affects cotreatment, decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
methyleugenol	decreases expression	1
arsenite	affects binding, increases reaction	1
4-phenylbutyric acid	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
deguelin	increases expression	1
ICG 001	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Air Pollutants	increases abundance, increases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Coumestrol	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylstilbestrol	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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