C9orf152

Summary

C9orf152 (chromosome 9 open reading frame 152, HGNC:31455) is a protein-coding gene on chromosome 9q31.3, encoding Uncharacterized protein C9orf152 (Q5JTZ5).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 7 total — 1 pathogenic
• MANE Select transcript: NM_001012993

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31455
Approved symbol	C9orf152
Name	chromosome 9 open reading frame 152
Location	9q31.3
Locus type	gene with protein product
Status	Approved
Aliases	bA470J20.2
Ensembl gene	ENSG00000188959
Ensembl biotype	protein_coding
Entrez	401546

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000400613, ENST00000473442

RefSeq mRNA: 1 — MANE Select: NM_001012993 NM_001012993

CCDS: CCDS35102

Canonical transcript exons

ENST00000400613 — 2 exons

Exon	Start	End
ENSE00001551179	110207387	110208159
ENSE00001847283	110199561	110201474

Expression profiles

Bgee: expression breadth ubiquitous, 148 present calls, max score 96.68.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8649 / max 66.6418, expressed in 165 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
101914	0.7450	162
101915	0.1198	32

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	96.68	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.22	gold quality
colonic mucosa	UBERON:0000317	92.86	gold quality
rectum	UBERON:0001052	92.81	gold quality
mucosa of transverse colon	UBERON:0004991	91.99	gold quality
pylorus	UBERON:0001166	87.02	gold quality
bronchial epithelial cell	CL:0002328	86.41	gold quality
bronchus	UBERON:0002185	85.69	gold quality
epithelial cell of pancreas	CL:0000083	84.67	gold quality
jejunal mucosa	UBERON:0000399	83.81	gold quality
cardia of stomach	UBERON:0001162	83.05	gold quality
lower lobe of lung	UBERON:0008949	82.81	gold quality
pancreatic ductal cell	CL:0002079	82.77	gold quality
nasal cavity epithelium	UBERON:0005384	82.53	gold quality
duodenum	UBERON:0002114	82.38	gold quality
parotid gland	UBERON:0001831	82.25	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	81.90	gold quality
colonic epithelium	UBERON:0000397	81.84	gold quality
saliva-secreting gland	UBERON:0001044	80.95	gold quality
body of stomach	UBERON:0001161	80.63	gold quality
stomach	UBERON:0000945	80.11	gold quality
minor salivary gland	UBERON:0001830	79.53	gold quality
nasal cavity mucosa	UBERON:0001826	79.47	gold quality
transverse colon	UBERON:0001157	79.31	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.33	gold quality
endometrium	UBERON:0001295	77.96	gold quality
prostate gland	UBERON:0002367	77.73	gold quality
trachea	UBERON:0003126	76.27	gold quality
gall bladder	UBERON:0002110	75.23	gold quality
mouth mucosa	UBERON:0003729	74.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting C9orf152, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4658	99.77	64.94	514

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	D630039A03Rik	ENSMUSG00000052117
rattus_norvegicus	C5h9orf152	ENSRNOG00000012068

Protein

Protein identifiers

Uncharacterized protein C9orf152 — Q5JTZ5 (reviewed: Q5JTZ5)

All UniProt accessions (1): Q5JTZ5

RefSeq proteins (1): NP_001013011* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032738	Tbc1d30_C	Domain

Pfam: PF15733

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JTZ5-F1	58.36	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): GOZGIT_ESR1_TARGETS_DN, RODRIGUES_NTN1_TARGETS_DN, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, GAVIN_FOXP3_TARGETS_CLUSTER_P7, BOCHKIS_FOXA2_TARGETS, DODD_NASOPHARYNGEAL_CARCINOMA_DN, WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MARTENS_TRETINOIN_RESPONSE_UP, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN, DELACROIX_RAR_BOUND_ES, RAO_BOUND_BY_SALL4, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP, GSE13522_WT_VS_IFNAR_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

288 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C9orf152	SMKR1	H3BMG3	506
C9orf152	RAB30	Q15771	480
C9orf152	SLFNL1	Q499Z3	474
C9orf152	PRR15L	Q9BU68	415
C9orf152	C1orf116	Q9BW04	411
C9orf152	KIAA0040	Q15053	410
C9orf152	SMCO1	Q147U7	395
C9orf152	ELAPOR1	Q6UXG2	394
C9orf152	PAK1IP1	Q9NWT1	381
C9orf152	ZNF385B	Q569K4	377
C9orf152	ENDOD1	O94919	367
C9orf152	TRIM48	Q8IWZ4	366
C9orf152	SOX8	P57073	358
C9orf152	TMEM252	Q8N6L7	348
C9orf152	TRIM51	Q9BSJ1	348

IntAct

8 interactions, top by confidence:

A	B	Type	Score
MLH1	C9orf152	psi-mi:“MI:0915”(physical association)	0.560
ANKS1A	C9orf152	psi-mi:“MI:0915”(physical association)	0.560
C9orf152	SEC24D	psi-mi:“MI:0914”(association)	0.350
ANKS1A	C9orf152	psi-mi:“MI:0915”(physical association)	0.000
MLH1	C9orf152	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): C9orf152 (Two-hybrid), C9orf152 (Two-hybrid), ZYG11B (Affinity Capture-MS), SEC24D (Affinity Capture-MS), PITRM1 (Affinity Capture-MS), C9orf152 (Positive Genetic)

ESM2 similar proteins: A0A1B0GVZ6, A5D7I0, A6H7B4, A6NDZ8, A6NE82, A6NJ08, A6NJB7, A6NJI1, A6NL46, A6QP24, A8MUA0, A8MUI8, A8MV72, A8MX80, B2RW88, O94850, P0C6A0, P24097, P50617, Q0P5M0, Q0VD86, Q2KIL8, Q3B8N5, Q3SY00, Q3SYA9, Q3UN58, Q5BMD4, Q5JTZ5, Q5RBE4, Q5VZ46, Q66MI6, Q68US1, Q6GQV0, Q6PAC4, Q80TS7, Q80VY2, Q8BFY7, Q8BII1, Q8IXW0, Q8K2F3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	0
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
394605	GRCh37/hg19 9q31.3-33.1(chr9:111348809-118687200)x1	Pathogenic

SpliceAI

331 predictions. Top by Δscore:

Variant	Effect	Δscore
9:110208036:AGAGC:A	donor_gain	1.0000
9:110201472:CTC:C	acceptor_gain	0.9900
9:110201474:CCTG:C	acceptor_loss	0.9900
9:110201475:C:CA	acceptor_loss	0.9900
9:110201475:C:CC	acceptor_gain	0.9900
9:110201476:T:A	acceptor_loss	0.9900
9:110207382:CCTA:C	donor_loss	0.9900
9:110207383:CTAC:C	donor_loss	0.9900
9:110207384:TA:T	donor_loss	0.9900
9:110207385:ACC:A	donor_loss	0.9900
9:110207386:C:CA	donor_loss	0.9900
9:110208029:G:C	donor_gain	0.9900
9:110208036:AGAG:A	donor_gain	0.9900
9:110208068:ATT:A	donor_gain	0.9900
9:110208080:T:TA	donor_gain	0.9900
9:110201470:TCCTC:T	acceptor_gain	0.9800
9:110201471:CCTCC:C	acceptor_gain	0.9800
9:110201473:TC:T	acceptor_gain	0.9800
9:110201474:CC:C	acceptor_gain	0.9800
9:110208068:A:AC	donor_gain	0.9800
9:110201471:CCTC:C	acceptor_gain	0.9700
9:110201472:CTCC:C	acceptor_gain	0.9700
9:110201473:TCCTG:T	acceptor_gain	0.9700
9:110208069:T:C	donor_gain	0.9600
9:110208076:T:TA	donor_gain	0.9600
9:110208081:C:A	donor_gain	0.9600
9:110208136:C:A	donor_gain	0.9600
9:110208141:T:A	donor_gain	0.9600
9:110208038:AGC:A	donor_gain	0.9500
9:110208070:T:TA	donor_gain	0.9500

AlphaMissense

1550 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:110201014:A:C	F218L	0.971
9:110201014:A:T	F218L	0.971
9:110201016:A:G	F218L	0.971
9:110200964:A:G	L235S	0.958
9:110200979:G:T	A230D	0.958
9:110200976:C:G	R231P	0.954
9:110201003:T:A	K222I	0.917
9:110201002:T:A	K222N	0.913
9:110201002:T:G	K222N	0.913
9:110201015:A:G	F218S	0.910
9:110201426:A:G	I81T	0.908
9:110200991:A:G	I226T	0.906
9:110200970:A:G	L233P	0.901
9:110201317:C:A	W117C	0.899
9:110201317:C:G	W117C	0.899
9:110200988:G:A	S227F	0.897
9:110201319:A:G	W117R	0.895
9:110201319:A:T	W117R	0.895
9:110200967:C:A	G234V	0.893
9:110200991:A:C	I226S	0.888
9:110200980:C:G	A230P	0.884
9:110201015:A:C	F218C	0.884
9:110201022:A:C	Y216D	0.882
9:110200967:C:T	G234D	0.868
9:110200989:A:G	S227P	0.864
9:110201426:A:C	I81S	0.860
9:110201003:T:G	K222T	0.858
9:110200968:C:G	G234R	0.857
9:110200993:C:A	R225S	0.857
9:110200993:C:G	R225S	0.857

dbSNP variants (sampled 300 via entrez): RS1000711500 (9:110206341 G>A,T), RS1000715514 (9:110199943 C>T), RS1000848744 (9:110205141 C>A), RS1000975402 (9:110199542 A>C), RS1001005171 (9:110199786 C>T), RS1001778736 (9:110205825 G>A,T), RS1001972785 (9:110199878 C>CT), RS1002050036 (9:110205351 A>G), RS1002418973 (9:110200513 A>C), RS1002475294 (9:110203078 G>A,T), RS1002716027 (9:110202804 G>A,C), RS1002992552 (9:110208861 A>G), RS1003110520 (9:110208444 C>T), RS1003222768 (9:110201564 A>T), RS1003707536 (9:110209663 G>T)

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

2 associations (top):

Study	Trait	p-value
GCST012490_49	Femur bone mineral density x serum urate levels interaction	2.000000e-11
GCST012490_560	Femur bone mineral density x serum urate levels interaction	1.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004531	urate measurement

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
Nickel	decreases expression	2
OTX015	decreases expression	1
mivebresib	decreases expression	1
dicrotophos	increases expression	1
propionaldehyde	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
butyraldehyde	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
pentanal	decreases expression	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Aldehydes	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Coumestrol	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Formaldehyde	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Quercetin	increases expression	1
Dihydrotestosterone	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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