SNORC

Summary

SNORC (secondary ossification center associated regulator of chondrocyte maturation, HGNC:33763) is a protein-coding gene on chromosome 2q37.1, encoding Protein SNORC (Q6UX34). Plays a role in the regulation of chondrocyte maturation and postnatal endochondral ossification.

Predicted to be involved in cartilage development. Predicted to be located in several cellular components, including collagen-containing extracellular matrix; cytoplasm; and extracellular region. Predicted to be active in cell periphery.

Source: NCBI Gene 389084 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001394206

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33763
Approved symbol	SNORC
Name	secondary ossification center associated regulator of chondrocyte maturation
Location	2q37.1
Locus type	gene with protein product
Status	Approved
Aliases	UNQ830, ASCL830
Ensembl gene	ENSG00000182600
Ensembl biotype	protein_coding
OMIM	620882
Entrez	389084

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000331342, ENST00000409230, ENST00000409533, ENST00000448993, ENST00000449331, ENST00000467665, ENST00000476690, ENST00000481155, ENST00000695538

RefSeq mRNA: 6 — MANE Select: NM_001394206 NM_001346120, NM_001346121, NM_001346122, NM_001394206, NM_001394207, NM_206895

CCDS: CCDS2499

Canonical transcript exons

ENST00000331342 — 3 exons

Exon	Start	End
ENSE00001300328	232876247	232878700
ENSE00001303967	232870264	232870414
ENSE00003601653	232875940	232876122

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 96.69.

FANTOM5 (CAGE): breadth broad, TPM avg 4.9082 / max 486.5193, expressed in 313 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26022	3.9649	273
26018	0.2509	46
26015	0.2211	73
26016	0.1722	31
26021	0.1517	81
26020	0.0595	28
26017	0.0500	15
26019	0.0379	26

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
spinal cord	UBERON:0002240	96.69	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.59	gold quality
inferior vagus X ganglion	UBERON:0005363	92.01	gold quality
medulla oblongata	UBERON:0001896	91.26	gold quality
ventral tegmental area	UBERON:0002691	90.48	gold quality
substantia nigra	UBERON:0002038	90.16	gold quality
hypothalamus	UBERON:0001898	90.14	gold quality
midbrain	UBERON:0001891	89.96	gold quality
mucosa of transverse colon	UBERON:0004991	89.61	gold quality
subthalamic nucleus	UBERON:0001906	88.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.74	gold quality
superior vestibular nucleus	UBERON:0007227	88.34	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.60	gold quality
ileal mucosa	UBERON:0000331	87.36	gold quality
putamen	UBERON:0001874	87.16	gold quality
tibia	UBERON:0000979	87.07	gold quality
caudate nucleus	UBERON:0001873	86.98	gold quality
right frontal lobe	UBERON:0002810	86.17	gold quality
Ammon’s horn	UBERON:0001954	86.16	gold quality
dorsal plus ventral thalamus	UBERON:0001897	85.72	gold quality
anterior cingulate cortex	UBERON:0009835	85.05	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.94	gold quality
skin of leg	UBERON:0001511	84.65	gold quality
upper arm skin	UBERON:0004263	84.02	gold quality
prefrontal cortex	UBERON:0000451	83.84	gold quality
frontal cortex	UBERON:0001870	83.54	gold quality
cerebral cortex	UBERON:0000956	83.27	gold quality
nucleus accumbens	UBERON:0001882	83.14	gold quality
neocortex	UBERON:0001950	83.08	gold quality
forebrain	UBERON:0001890	82.73	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-9841	yes	749.72
E-GEOD-125970	yes	40.55
E-CURD-112	yes	6.20
E-ANND-3	yes	5.76

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Attention-deficit/hyperactivity disorder (ADHD) risk alleles correlated with increased expression (and decreased methylation) of ARTN and PIDD1 and with a decreased expression (and increased methylation) of C2orf82. (PMID:31582733)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Snorc	ENSMUSG00000026258
rattus_norvegicus	Snorc	ENSRNOG00000084451

Protein

Protein identifiers

Protein SNORC — Q6UX34 (reviewed: Q6UX34)

Alternative names: Secondary ossification center-associated regulator of chondrocyte maturation protein

All UniProt accessions (3): Q6UX34, A0A6M4NK13, C9K0N5

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the regulation of chondrocyte maturation and postnatal endochondral ossification. May inhibit cell growth stimulation induced by FGF2.

Subunit / interactions. Interacts (via the extracellular domain) with FGF2.

Subcellular location. Membrane. Cytoplasm. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Expressed in cartilage.

RefSeq proteins (6): NP_001333049, NP_001333050, NP_001333051, NP_001381135, NP_001381136, NP_996778 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031500	SNORC	Family

Pfam: PF15756

UniProt features (6 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UX34-F1	65.58	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 51 (showing top): RNGTGGGC_UNKNOWN, GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, GRE_C, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, MARTENS_TRETINOIN_RESPONSE_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, LIM_MAMMARY_STEM_CELL_DN, DLX2_TARGET_GENES, FOXN3_TARGET_GENES, HES2_TARGET_GENES, HMG20B_TARGET_GENES

GO Biological Process (1): cartilage development (GO:0051216)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): cytoplasm (GO:0005737), membrane (GO:0016020), cell periphery (GO:0071944), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
skeletal system development	1
animal organ development	1
connective tissue development	1
binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

238 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNORC	COL9A1	P20849	410
SNORC	WDR73	Q6P4I2	393
SNORC	GTPBP2	Q9BX10	381
SNORC	ZNF385C	Q66K41	375
SNORC	CLEC3A	O75596	372
SNORC	OGFOD2	Q6N063	348
SNORC	ACAN	P16112	348
SNORC	MATN4	O95460	325
SNORC	CYTL1	Q9NRR1	324
SNORC	MFAP4	P55083	323
SNORC	SLC75A1	Q14728	320
SNORC	MPG	P29372	316
SNORC	TTC39B	Q5VTQ0	316
SNORC	COL10A1	Q03692	313
SNORC	C16orf54	Q6UWD8	310

IntAct

70 interactions, top by confidence:

A	B	Type	Score
SNORC	HSD17B13	psi-mi:“MI:0915”(physical association)	0.560
SNORC	SLC14A1	psi-mi:“MI:0915”(physical association)	0.560
SNORC	KIR2DL3	psi-mi:“MI:0915”(physical association)	0.560
SNORC	SLC10A6	psi-mi:“MI:0915”(physical association)	0.560
SNORC	ELOVL4	psi-mi:“MI:0915”(physical association)	0.560
SNORC	CISD2	psi-mi:“MI:0915”(physical association)	0.560
SNORC	GPX8	psi-mi:“MI:0915”(physical association)	0.560
SNORC	LHFPL2	psi-mi:“MI:0915”(physical association)	0.560
SNORC	HIBADH	psi-mi:“MI:0915”(physical association)	0.560
STX1A	SNORC	psi-mi:“MI:0915”(physical association)	0.560
SNORC	SLC26A6	psi-mi:“MI:0915”(physical association)	0.560
	SNORC	psi-mi:“MI:0915”(physical association)	0.560
SNORC	LRRC59	psi-mi:“MI:0915”(physical association)	0.560
SNORC	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
EBP	SNORC	psi-mi:“MI:0915”(physical association)	0.560
SNORC	SLC7A8	psi-mi:“MI:0915”(physical association)	0.560
CD53	SNORC	psi-mi:“MI:0915”(physical association)	0.560
SLC14A1	SNORC	psi-mi:“MI:0915”(physical association)	0.560
KIR2DL3	SNORC	psi-mi:“MI:0915”(physical association)	0.560
MGST3	SNORC	psi-mi:“MI:0915”(physical association)	0.560
SLC10A6	SNORC	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (26): C2orf82 (Affinity Capture-RNA), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid), C2orf82 (Two-hybrid)

ESM2 similar proteins: A0A5F4BST2, A5PJC7, A8MWV9, D3ZZP4, O14836, P0CAN6, P11911, P11912, P14753, Q01114, Q07303, Q13113, Q2KI80, Q2KL21, Q3TS39, Q3URD2, Q4V9L6, Q5F267, Q5FVJ4, Q5FVQ7, Q5RA41, Q5T1S8, Q6P9G4, Q6UWJ8, Q6UX34, Q80VJ8, Q810F0, Q86XR5, Q8BRJ3, Q8BX43, Q8K064, Q8K5A9, Q8N112, Q8N4K4, Q8N6L0, Q8NBR0, Q8NC24, Q8QZT4, Q8R138, Q923S2

Diamond homologs: Q6UX34, Q9CXL7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

493 predictions. Top by Δscore:

Variant	Effect	Δscore
2:232875938:A:AG	acceptor_gain	1.0000
2:232875938:AG:A	acceptor_loss	1.0000
2:232875938:AGAC:A	acceptor_gain	1.0000
2:232875939:G:GG	acceptor_gain	1.0000
2:232875939:GAC:G	acceptor_gain	1.0000
2:232875939:GACG:G	acceptor_gain	1.0000
2:232875939:GACGA:G	acceptor_gain	1.0000
2:232876101:G:GT	donor_gain	1.0000
2:232876102:A:T	donor_gain	1.0000
2:232876116:G:GT	donor_gain	1.0000
2:232876119:GGCG:G	donor_gain	1.0000
2:232876120:GCGG:G	donor_gain	1.0000
2:232876121:CGGTA:C	donor_loss	1.0000
2:232876122:GGTAC:G	donor_loss	1.0000
2:232876123:G:GA	donor_loss	1.0000
2:232876123:G:GG	donor_gain	1.0000
2:232876124:T:G	donor_loss	1.0000
2:232876245:AG:A	acceptor_gain	1.0000
2:232876246:GG:G	acceptor_gain	1.0000
2:232869098:TAGG:T	donor_loss	0.9900
2:232869100:GG:G	donor_gain	0.9900
2:232869101:GG:G	donor_gain	0.9900
2:232869103:T:A	donor_loss	0.9900
2:232875939:GA:G	acceptor_gain	0.9900
2:232876086:G:GT	donor_gain	0.9900
2:232876117:G:T	donor_gain	0.9900
2:232876120:GCG:G	donor_gain	0.9900
2:232876241:CCGCA:C	acceptor_loss	0.9900
2:232876242:CGCA:C	acceptor_loss	0.9900
2:232876243:GCAGG:G	acceptor_loss	0.9900

AlphaMissense

741 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:232876303:T:C	C105R	0.998
2:232876319:T:A	L110H	0.998
2:232876286:C:A	A99D	0.997
2:232876295:T:A	L102Q	0.995
2:232876289:C:A	A100D	0.993
2:232876274:C:A	A95D	0.992
2:232876277:T:A	I96N	0.992
2:232876295:T:G	L102R	0.991
2:232876319:T:C	L110P	0.991
2:232876283:T:A	I98N	0.990
2:232876298:C:A	A103D	0.990
2:232876316:C:A	A109E	0.989
2:232876319:T:G	L110R	0.989
2:232876304:G:A	C105Y	0.988
2:232876307:T:A	V106E	0.987
2:232876268:T:A	I93N	0.984
2:232876295:T:C	L102P	0.984
2:232876328:T:A	V113D	0.984
2:232876325:T:A	V112D	0.983
2:232876292:T:G	L101R	0.981
2:232876305:C:G	C105W	0.980
2:232876271:C:A	A94E	0.978
2:232876288:G:C	A100P	0.978
2:232876273:G:C	A95P	0.977
2:232876280:T:A	V97E	0.977
2:232876331:C:A	A114E	0.976
2:232876342:T:C	F118L	0.976
2:232876344:T:A	F118L	0.976
2:232876344:T:G	F118L	0.976
2:232876277:T:G	I96S	0.975

dbSNP variants (sampled 300 via entrez): RS1000254568 (2:232875748 C>T), RS1000304389 (2:232875538 A>G,T), RS1000779742 (2:232866040 A>T), RS1000984549 (2:232871395 C>T), RS1001091032 (2:232866078 G>T), RS1001205442 (2:232877237 T>G), RS1001493716 (2:232876349 C>T), RS1001505640 (2:232871626 C>T), RS1001607974 (2:232870935 G>A), RS1001787131 (2:232871962 C>T), RS1001819549 (2:232877366 T>C), RS1001875260 (2:232876966 C>A), RS1001987601 (2:232871795 G>A), RS1002058561 (2:232870623 G>A), RS1002094220 (2:232876967 G>A,C)

Disease associations

OMIM: gene MIM:620882 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002149_18	Schizophrenia	2.000000e-08
GCST002539_44	Schizophrenia	2.000000e-12
GCST004521_189	Autism spectrum disorder or schizophrenia	3.000000e-10
GCST004521_38	Autism spectrum disorder or schizophrenia	1.000000e-08
GCST004946_89	Schizophrenia	2.000000e-13
GCST006803_9	Schizophrenia	4.000000e-16
GCST008103_148	Bipolar disorder	3.000000e-06
GCST009600_12	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, increases methylation	1
dicrotophos	decreases expression	1
bisphenol A	affects methylation	1
methylparaben	decreases expression	1
butyraldehyde	increases expression	1
K 7174	decreases expression	1
ICG 001	increases expression	1
jinfukang	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	decreases expression	1
Arsenicals	decreases expression	1
Niclosamide	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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