C9orf153

Summary

C9orf153 (chromosome 9 open reading frame 153, HGNC:31456) is a protein-coding gene on chromosome 9q21.33, encoding Uncharacterized protein C9orf153 (Q5TBE3).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001276366

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31456
Approved symbol	C9orf153
Name	chromosome 9 open reading frame 153
Location	9q21.33
Locus type	gene with protein product
Status	Approved
Aliases	bA507D14.1
Ensembl gene	ENSG00000187753
Ensembl biotype	protein_coding
Entrez	389766

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000339137, ENST00000376001, ENST00000469914, ENST00000613665, ENST00000617985, ENST00000649213

RefSeq mRNA: 3 — MANE Select: NM_001276366 NM_001276366, NM_001276367, NM_001276368

CCDS: CCDS35055

Canonical transcript exons

ENST00000339137 — 4 exons

Exon	Start	End
ENSE00001373858	86227855	86228030
ENSE00001390681	86220265	86221733
ENSE00001469109	86259550	86259657
ENSE00003495072	86229538	86229629

Expression profiles

Bgee: expression breadth ubiquitous, 105 present calls, max score 85.58.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0181 / max 16.6901, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
101203	0.0137	3
101204	0.0044	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	85.58	gold quality
right testis	UBERON:0004534	85.38	gold quality
testis	UBERON:0000473	85.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.35	gold quality
placenta	UBERON:0001987	59.30	gold quality
calcaneal tendon	UBERON:0003701	55.25	gold quality
sural nerve	UBERON:0015488	55.05	gold quality
apex of heart	UBERON:0002098	54.36	gold quality
corpus callosum	UBERON:0002336	53.53	gold quality
colonic epithelium	UBERON:0000397	53.04	silver quality
blood	UBERON:0000178	51.64	gold quality
bone marrow cell	CL:0002092	50.23	gold quality
adrenal tissue	UBERON:0018303	49.36	gold quality
lung	UBERON:0002048	48.88	gold quality
skeletal muscle tissue	UBERON:0001134	48.63	silver quality
bone marrow	UBERON:0002371	48.27	silver quality
islet of Langerhans	UBERON:0000006	48.22	gold quality
liver	UBERON:0002107	47.51	silver quality
mucosa of transverse colon	UBERON:0004991	46.97	gold quality
muscle tissue	UBERON:0002385	46.95	gold quality
monocyte	CL:0000576	46.82	gold quality
upper lobe of left lung	UBERON:0008952	46.72	gold quality
right lung	UBERON:0002167	46.65	gold quality
endometrium	UBERON:0001295	45.89	gold quality
leukocyte	CL:0000738	45.61	gold quality
right lobe of liver	UBERON:0001114	45.24	gold quality
heart left ventricle	UBERON:0002084	44.21	gold quality
omental fat pad	UBERON:0010414	43.91	gold quality
uterine cervix	UBERON:0000002	43.82	gold quality
heart	UBERON:0000948	43.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.36

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Uncharacterized protein C9orf153 — Q5TBE3 (reviewed: Q5TBE3)

All UniProt accessions (2): A0A3B3ISE1, Q5TBE3

Isoforms (2)

UniProt ID	Names	Canonical?
Q5TBE3-1	1	yes
Q5TBE3-2	2

RefSeq proteins (3): NP_001263295, NP_001263296, NP_001263297 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040022	C9orf153-like	Family

Pfam: PF17673

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TBE3-F1	65.26	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): chr9q21, DELACROIX_RAR_BOUND_ES, RAO_BOUND_BY_SALL4_ISOFORM_B, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, SUPT16H_TARGET_GENES, MIR4795_3P, MIR6844, MIR5010_3P, MIR4503, MIR205_5P, MIR4743_3P, MIR6795_5P, MIR6887_5P, MIR1244, MIR647

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

106 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C9orf153	MAGEB5	Q9BZ81	541
C9orf153	CCDC125	Q86Z20	514
C9orf153	ARSG	Q96EG1	508
C9orf153	FAM81A	Q8TBF8	507
C9orf153	NUP210L	Q5VU65	505
C9orf153	COPS7B	Q9H9Q2	418
C9orf153	NAA35	Q5VZE5	417
C9orf153	KIF27	Q86VH2	398
C9orf153	TBCK	Q8TEA7	397
C9orf153	KCNAB3	O43448	371
C9orf153	IDI2	Q9BXS1	370
C9orf153	STXBP5L	Q9Y2K9	369
C9orf153	POLN	Q7Z5Q5	367
C9orf153	AGTPBP1	Q9UPW5	366
C9orf153	PSORS1C1	Q9UIG5	359

IntAct

1 interactions, top by confidence:

BioGRID (3): C6orf165 (Two-hybrid), C9orf153 (Positive Genetic), C9orf153 (Positive Genetic)

ESM2 similar proteins: A0T0Z7, A1T8H5, A3M5C1, A4X624, A6WCB6, A7MMM5, A8LE17, A8LY23, B0VDY4, B0VPM5, B1XPU8, B2I0B1, B3PK41, B7H3B2, B7I5W1, B8ZUM0, C5D4K0, C5E3I1, O30315, O41126, O43018, O64233, O68557, O83053, P02660, P03516, P04030, P0C1A0, P20402, P26146, P31182, P31192, P43395, P55695, P68395, Q00247, Q01RT2, Q04262, Q07032, Q07049

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

602 predictions. Top by Δscore:

Variant	Effect	Δscore
9:86229536:A:AC	donor_gain	1.0000
9:86229537:C:CC	donor_gain	1.0000
9:86227789:G:A	donor_gain	0.9900
9:86227933:T:TA	donor_gain	0.9900
9:86229533:CATA:C	donor_gain	0.9900
9:86229537:CTGAA:C	donor_gain	0.9900
9:86259548:A:AC	donor_gain	0.9900
9:86259549:C:CC	donor_gain	0.9900
9:86259549:CCA:C	donor_gain	0.9900
9:86259544:ACTT:A	donor_loss	0.9800
9:86259546:TTACC:T	donor_loss	0.9800
9:86259547:TACC:T	donor_gain	0.9800
9:86259548:ACCA:A	donor_gain	0.9800
9:86259549:C:G	donor_loss	0.9800
9:86259549:CCAC:C	donor_gain	0.9800
9:86259549:CCACT:C	donor_gain	0.9800
9:86227934:C:A	donor_gain	0.9700
9:86259546:TTAC:T	donor_gain	0.9700
9:86234871:G:C	donor_gain	0.9600
9:86259548:AC:A	donor_gain	0.9500
9:86259549:CC:C	donor_gain	0.9500
9:86227641:TGGA:T	donor_gain	0.9400
9:86229541:A:C	donor_gain	0.9400
9:86239179:TGA:T	donor_gain	0.9400
9:86229529:A:C	donor_gain	0.8300
9:86245538:G:C	donor_gain	0.8300
9:86227884:A:C	donor_gain	0.8200
9:86229209:AG:A	acceptor_gain	0.8200
9:86259545:CTTA:C	donor_gain	0.8200
9:86229500:C:CA	donor_gain	0.8100

AlphaMissense

623 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:86228020:A:G	L26S	0.852
9:86227940:C:G	A53P	0.817
9:86227998:A:C	F33L	0.816
9:86227998:A:T	F33L	0.816
9:86228000:A:G	F33L	0.816
9:86228029:A:T	L23H	0.740
9:86227939:G:T	A53E	0.728
9:86227927:A:T	L57H	0.701
9:86228029:A:G	L23P	0.688
9:86227972:A:G	L42P	0.678
9:86227999:A:G	F33S	0.670
9:86227983:C:A	K38N	0.657
9:86227983:C:G	K38N	0.657
9:86228018:A:C	Y27D	0.645
9:86228029:A:C	L23R	0.643
9:86228008:A:T	I30N	0.620
9:86229598:G:C	F2L	0.618
9:86229598:G:T	F2L	0.618
9:86229600:A:G	F2L	0.618
9:86228015:C:G	A28P	0.608
9:86227927:A:C	L57R	0.604
9:86227927:A:G	L57P	0.602
9:86229543:A:G	C21R	0.588
9:86228017:T:G	Y27S	0.587

dbSNP variants (sampled 300 via entrez): RS1000033238 (9:86248663 C>A,G), RS1000135746 (9:86259654 C>A), RS1000296061 (9:86235052 C>T), RS1000375751 (9:86253351 A>G), RS1000439547 (9:86228925 C>A,G), RS1000476596 (9:86246298 G>A,C,T), RS1000497128 (9:86222713 A>C,G), RS1000570355 (9:86223165 C>G), RS1000647963 (9:86229264 A>AG), RS1000662402 (9:86253053 C>T), RS1000676304 (9:86223133 C>T), RS1000769143 (9:86259962 C>T), RS1000943700 (9:86241628 G>A), RS1000956416 (9:86228941 C>T), RS1000962586 (9:86235008 C>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

3 associations (top):

Study	Trait	p-value
GCST007006_7	Logical memory (delayed recall) in normal cognition	2.000000e-07
GCST010819_12	Gut microbiota alpha diversity (Chao1 index)	6.000000e-06
GCST90002385_384	High light scatter reticulocyte count	1.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance
EFO:0007874	gut microbiome measurement
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium	increases abundance, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Rifampin	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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