SSUH2

Summary

SSUH2 (ssu-2 homolog, HGNC:24809) is a protein-coding gene on chromosome 3p25.3, encoding Protein SSUH2 homolog (Q9Y2M2). Plays a role in odontogenesis.

Predicted to enable heat shock protein binding activity and unfolded protein binding activity. Involved in odontogenesis. Located in cytoplasm and nucleus.

Source: NCBI Gene 51066 — RefSeq curated summary.

At a glance

• Gene–disease (curated): dentin dysplasia type I (Supportive, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 70 total — 1 pathogenic
• MANE Select transcript: NM_001256748

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24809
Approved symbol	SSUH2
Name	ssu-2 homolog
Location	3p25.3
Locus type	gene with protein product
Status	Approved
Aliases	fls485, ssu-2
Ensembl gene	ENSG00000125046
Ensembl biotype	protein_coding
OMIM	617479
Entrez	51066

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 6 protein_coding_CDS_not_defined, 5 protein_coding, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000317371, ENST00000341795, ENST00000413305, ENST00000415132, ENST00000420394, ENST00000435138, ENST00000455157, ENST00000464494, ENST00000466215, ENST00000470009, ENST00000478513, ENST00000483845, ENST00000484585, ENST00000492435, ENST00000495366, ENST00000544814

RefSeq mRNA: 3 — MANE Select: NM_001256748 NM_001256748, NM_001256749, NM_015931

CCDS: CCDS2568, CCDS58815

Canonical transcript exons

ENST00000544814 — 12 exons

Exon	Start	End
ENSE00003481373	8632049	8632109
ENSE00003485872	8635300	8635381
ENSE00003487319	8629664	8629726
ENSE00003528290	8630805	8630929
ENSE00003539779	8644731	8644798
ENSE00003548025	8635759	8635857
ENSE00003548692	8623549	8623656
ENSE00003582216	8633666	8633795
ENSE00003640628	8627698	8627783
ENSE00003668081	8626229	8626321
ENSE00003678512	8625542	8625647
ENSE00003851439	8619386	8620014

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 93.85.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3822 / max 86.7036, expressed in 65 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
40931	0.2316	18
40928	0.1031	45
40929	0.0246	9
40930	0.0229	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	93.85	gold quality
male germ cell	CL:0000015	91.19	gold quality
jejunal mucosa	UBERON:0000399	86.31	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.78	gold quality
right testis	UBERON:0004534	84.72	gold quality
left testis	UBERON:0004533	84.23	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.64	gold quality
testis	UBERON:0000473	81.83	gold quality
duodenum	UBERON:0002114	80.31	gold quality
ileal mucosa	UBERON:0000331	77.38	silver quality
mucosa of paranasal sinus	UBERON:0005030	75.72	silver quality
small intestine Peyer’s patch	UBERON:0003454	74.17	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.84	gold quality
small intestine	UBERON:0002108	73.78	gold quality
endothelial cell	CL:0000115	73.25	silver quality
apex of heart	UBERON:0002098	72.84	gold quality
bronchial epithelial cell	CL:0002328	72.51	gold quality
epithelium of bronchus	UBERON:0002031	71.56	silver quality
bronchus	UBERON:0002185	70.46	silver quality
heart left ventricle	UBERON:0002084	68.93	gold quality
cardiac ventricle	UBERON:0002082	68.48	gold quality
jejunum	UBERON:0002115	67.57	gold quality
epithelium of nasopharynx	UBERON:0001951	67.02	silver quality
tibia	UBERON:0000979	66.62	silver quality
right atrium auricular region	UBERON:0006631	66.18	gold quality
heart	UBERON:0000948	65.45	gold quality
secondary oocyte	CL:0000655	65.35	gold quality
cardiac atrium	UBERON:0002081	64.96	gold quality
spleen	UBERON:0002106	64.85	gold quality
gall bladder	UBERON:0002110	64.55	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting SSUH2, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-143-5P	98.98	68.87	946
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-4680-3P	98.64	68.60	2093
HSA-MIR-7156-3P	98.25	67.66	859
HSA-MIR-3936	97.64	64.47	732
HSA-MIR-320E	97.49	65.96	865
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-6895-5P	97.05	64.96	522
HSA-MIR-212-5P	96.83	67.43	950

Literature-anchored findings (GeneRIF, showing 2)

• Expression and synthesis of fls485 are found in surface lining epithelia of normal human intestinal mucosa and deriving epithelial cell lines. (PMID:20205943)
• our observations demonstrate that SSUH2 disrupts dental formation and that this novel gene, together with other odontogenesis genes, is involved in tooth development. (PMID:27680507)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ssuh2.1	ENSDARG00000040938
mus_musculus	Ssu2	ENSMUSG00000034387
rattus_norvegicus	Ssuh2	ENSRNOG00000005734

Protein

Protein identifiers

Protein SSUH2 homolog — Q9Y2M2 (reviewed: Q9Y2M2)

Alternative names: Protein ssu-2 homolog

All UniProt accessions (7): A0A8V8TMK3, C9JAQ0, Q9Y2M2, F8WDP2, F8WDV4, F8WED9, G5E9S6

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in odontogenesis.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed in enterocytes of small and large intestinal mucosa (at protein level). Expressed in chromaffine and interstitial cells. Expressed in peripheral blood and gingival cells.

Disease relevance. Defects in SSUH2 are associated with dentin dysplasia, a genetic disorder characterized by severe tooth hypermobility, short dental roots, and obliterated pulp chambers.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y2M2-2	2	yes
Q9Y2M2-1	1
Q9Y2M2-3	3

RefSeq proteins (3): NP_001243677, NP_001243678, NP_057015 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001305	HSP_DnaJ_Cys-rich_dom	Domain
IPR052789	SSUH2_homolog	Family

UniProt features (6 total): splice variant 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2M2-F1	80.93	0.60

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, SCHLOSSER_SERUM_RESPONSE_DN, GOBP_ODONTOGENESIS, GOMF_HEAT_SHOCK_PROTEIN_BINDING, GOMF_UNFOLDED_PROTEIN_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, PR_Q2, RAPA_EARLY_UP.V1_UP, GLI1_TARGET_GENES, HMG20B_TARGET_GENES, NFKBIA_TARGET_GENES, ZNF436_TARGET_GENES, ZNF768_TARGET_GENES

GO Biological Process (1): odontogenesis (GO:0042476)

GO Molecular Function (3): heat shock protein binding (GO:0031072), obsolete unfolded protein binding (GO:0051082), 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
animal organ morphogenesis	1
protein binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

352 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSUH2	VPS4B	O75351	535
SSUH2	DYNLT5	Q8N7M0	527
SSUH2	SMOC2	Q9H3U7	464
SSUH2	A0A096LNW4	A0A096LNW4	440
SSUH2	ACP4	Q9BZG2	431
SSUH2	FANCD2OS	Q96PS1	419
SSUH2	M0QYU9	M0QYU9	419
SSUH2	SMIM7	Q9BQ49	399
SSUH2	ZNF587B	E7ETH6	398
SSUH2	LMCD1	Q9NZU5	379
SSUH2	PRRT3	Q5FWE3	378
SSUH2	SDR16C5	Q8N3Y7	369
SSUH2	HABP4	Q5JVS0	360
SSUH2	OGDHL	Q9ULD0	358
SSUH2	POTEI	P0CG38	356

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SSUH2	CNN1	psi-mi:“MI:0915”(physical association)	0.400
SSUH2	IGLC7	psi-mi:“MI:0914”(association)	0.350
CDC5L		psi-mi:“MI:0914”(association)	0.350
	SSUH2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (198): SSUH2 (Affinity Capture-MS), SSUH2 (Two-hybrid), SSUH2 (Two-hybrid), SSUH2 (Two-hybrid), CNN1 (Affinity Capture-MS), ACOX1 (Affinity Capture-MS), IL36RN (Affinity Capture-MS), HMGCS1 (Affinity Capture-MS), LTF (Affinity Capture-MS), SERPINA3 (Affinity Capture-MS), HIST1H1B (Affinity Capture-MS), NEFH (Affinity Capture-MS), EPS8L1 (Affinity Capture-MS), HAL (Affinity Capture-MS), UBLCP1 (Affinity Capture-MS)

ESM2 similar proteins: A1L3T7, A4IFR8, A6H5X4, A7E3N7, D3ZND0, E6ZIJ1, O13034, O70173, O94812, P51449, P51450, Q149G0, Q1L5Z9, Q1LZ50, Q3UMR0, Q400C9, Q400G9, Q4KLN4, Q5I0E2, Q5I0J8, Q5R8S0, Q5SY16, Q69ZT1, Q6AYG1, Q6R653, Q6ZV50, Q7TSG2, Q80TT2, Q86UW9, Q8BVF9, Q8BVM9, Q8C3L1, Q8C8H8, Q8CJ00, Q8JZL1, Q8N163, Q8QHJ9, Q8R322, Q8R3P2, Q8VDP4

Diamond homologs: Q08C76, Q8C3L1, Q9Y2M2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	55
Likely benign	6
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4819967	NM_001256748.3(SSUH2):c.419C>A (p.Pro140Gln)	Pathogenic

SpliceAI

2768 predictions. Top by Δscore:

Variant	Effect	Δscore
3:8625541:CCA:C	donor_gain	1.0000
3:8632047:A:AC	donor_gain	1.0000
3:8632048:C:CC	donor_gain	1.0000
3:8632105:CGGTA:C	acceptor_gain	1.0000
3:8632108:TA:T	acceptor_gain	1.0000
3:8632110:C:CC	acceptor_gain	1.0000
3:8633664:AC:A	donor_gain	1.0000
3:8633665:CC:C	donor_gain	1.0000
3:8633665:CCCTG:C	donor_gain	1.0000
3:8635757:A:AC	donor_gain	1.0000
3:8635757:ACTG:A	donor_gain	1.0000
3:8635757:ACTGC:A	donor_gain	1.0000
3:8635758:C:CC	donor_gain	1.0000
3:8635758:CTG:C	donor_gain	1.0000
3:8635758:CTGC:C	donor_gain	1.0000
3:8635758:CTGCC:C	donor_gain	1.0000
3:8733989:AGG:A	donor_loss	1.0000
3:8733991:GTA:G	donor_loss	1.0000
3:8620010:TGGCG:T	acceptor_gain	0.9900
3:8620013:CG:C	acceptor_gain	0.9900
3:8620015:C:CC	acceptor_gain	0.9900
3:8623456:T:TA	donor_gain	0.9900
3:8623653:ACACC:A	acceptor_loss	0.9900
3:8623654:CAC:C	acceptor_gain	0.9900
3:8623656:CCTG:C	acceptor_loss	0.9900
3:8623658:T:G	acceptor_loss	0.9900
3:8625555:T:TA	donor_gain	0.9900
3:8630930:C:CC	acceptor_gain	0.9900
3:8632041:TCAC:T	donor_loss	0.9900
3:8632042:CACT:C	donor_loss	0.9900

AlphaMissense

2456 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:8620013:C:G	R306P	0.993
3:8630853:A:C	F137L	0.991
3:8630853:A:T	F137L	0.991
3:8630855:A:G	F137L	0.991
3:8623550:T:G	Q305P	0.989
3:8629723:A:G	C155R	0.988
3:8626277:C:G	C218S	0.987
3:8626278:A:T	C218S	0.987
3:8626277:C:T	C218Y	0.986
3:8632080:C:A	R101S	0.986
3:8632080:C:G	R101S	0.986
3:8626287:A:G	C215R	0.985
3:8632105:C:G	R93P	0.985
3:8632092:A:C	F97L	0.984
3:8632092:A:T	F97L	0.984
3:8632094:A:G	F97L	0.984
3:8623549:C:A	Q305H	0.982
3:8623549:C:G	Q305H	0.982
3:8626259:A:G	L224P	0.982
3:8629713:C:G	C158S	0.982
3:8629714:A:T	C158S	0.982
3:8629722:C:G	C155S	0.982
3:8629723:A:T	C155S	0.982
3:8626278:A:G	C218R	0.981
3:8626277:C:A	C218F	0.980
3:8632109:A:C	Y92D	0.980
3:8620004:A:T	I309N	0.979
3:8626276:G:C	C218W	0.979
3:8625647:C:A	W234C	0.977
3:8625647:C:G	W234C	0.977

dbSNP variants (sampled 300 via entrez): RS1000064153 (3:8682213 A>C,G), RS1000074310 (3:8682124 T>C), RS1000089964 (3:8637494 C>T), RS1000157846 (3:8649443 A>G), RS1000165863 (3:8670520 A>C), RS1000183337 (3:8647979 G>A,T), RS1000186187 (3:8662333 T>C), RS1000286150 (3:8677902 C>T), RS1000290352 (3:8628919 G>A,C,T), RS1000373416 (3:8673836 A>T), RS1000380554 (3:8638859 G>A,C,T), RS1000385260 (3:8653084 C>G), RS1000484902 (3:8647708 C>T), RS1000485932 (3:8672179 T>C), RS1000558255 (3:8634927 A>T)

Disease associations

OMIM: gene MIM:617479 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
dentin dysplasia type I	Supportive	Autosomal dominant

Mondo (1): dentin dysplasia type I (MONDO:0007436)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008460_7	Gout vs. Hyperuricemia	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009104	hyperuricemia

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C538215	Dentin dysplasia, type 1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	increases expression, affects cotreatment	2
Benzo(a)pyrene	decreases expression, decreases methylation, increases methylation	2
Tetrachlorodibenzodioxin	decreases expression	2
Cadmium Chloride	decreases expression, increases abundance	2
bisphenol A	increases methylation, affects cotreatment	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
tobacco tar	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	affects cotreatment, increases expression	1
Allergens	affects cotreatment, decreases expression, increases abundance	1
Vehicle Emissions	decreases expression, increases abundance, affects cotreatment	1
Cadmium	decreases expression, increases abundance	1
Cytarabine	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Perfume	increases expression	1
Quercetin	decreases expression	1
Smoke	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation	1
Oxyquinoline	increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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