C11orf98

Summary

C11orf98 (chromosome 11 open reading frame 98, HGNC:51238) is a protein-coding gene on chromosome 11q12.3, encoding Uncharacterized protein C11orf98 (E9PRG8).

This gene shares three exons in common with another gene, LBH domain containing 1 (GeneID:79081), but the encoded protein uses a reading frame that is different from that of the LBH domain containing 1 gene.

Source: NCBI Gene 102288414 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_001286086

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51238
Approved symbol	C11orf98
Name	chromosome 11 open reading frame 98
Location	11q12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000278615
Ensembl biotype	protein_coding
Entrez	102288414

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000524958, ENST00000525675, ENST00000532786

RefSeq mRNA: 1 — MANE Select: NM_001286086 NM_001286086

CCDS: CCDS73306

Canonical transcript exons

ENST00000524958 — 4 exons

Exon	Start	End
ENSE00002146082	62665131	62665210
ENSE00003566048	62664849	62664973
ENSE00003606351	62663236	62663333
ENSE00003662213	62662817	62663159

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 78.3893 / max 448.9475, expressed in 1826 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120186	78.3893	1826

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	97.91	gold quality
granulocyte	CL:0000094	96.83	gold quality
lymph node	UBERON:0000029	96.11	gold quality
substantia nigra	UBERON:0002038	96.04	gold quality
right adrenal gland	UBERON:0001233	95.97	gold quality
lower esophagus mucosa	UBERON:0035834	95.85	gold quality
right testis	UBERON:0004534	95.83	gold quality
vermiform appendix	UBERON:0001154	95.77	gold quality
left testis	UBERON:0004533	95.67	gold quality
spleen	UBERON:0002106	95.62	gold quality
monocyte	CL:0000576	95.61	gold quality
leukocyte	CL:0000738	95.61	gold quality
right adrenal gland cortex	UBERON:0035827	95.61	gold quality
putamen	UBERON:0001874	95.55	gold quality
amygdala	UBERON:0001876	95.48	gold quality
body of stomach	UBERON:0001161	95.44	gold quality
hypothalamus	UBERON:0001898	95.39	gold quality
temporal lobe	UBERON:0001871	95.37	gold quality
testis	UBERON:0000473	95.31	gold quality
nucleus accumbens	UBERON:0001882	95.27	gold quality
anterior cingulate cortex	UBERON:0009835	95.24	gold quality
prefrontal cortex	UBERON:0000451	95.23	gold quality
esophagus mucosa	UBERON:0002469	95.23	gold quality
left adrenal gland	UBERON:0001234	95.11	gold quality
caudate nucleus	UBERON:0001873	95.11	gold quality
transverse colon	UBERON:0001157	95.08	gold quality
adult mammalian kidney	UBERON:0000082	95.05	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.04	gold quality
left adrenal gland cortex	UBERON:0035825	95.04	gold quality
prostate gland	UBERON:0002367	94.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting C11orf98, 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-4779	99.86	66.50	1583
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-4695-5P	99.06	64.87	1151
HSA-MIR-4266	98.53	67.29	1035
HSA-MIR-3158-3P	98.45	64.25	560
HSA-MIR-15A-3P	97.47	65.08	527
HSA-MIR-5704	94.82	67.46	448

Literature-anchored findings (GeneRIF, showing 1)

• Data suggest that C11orf98 microprotein, NPM1, and nucleolin interact and colocalize in the cell nucleolus. (C11orf98 = chromosome 11 open reading frame 98 protein; NPM1 = nucleophosmin 1) (PMID:28589727)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1810009A15Rik	ENSMUSG00000071653
rattus_norvegicus	C1h11orf98	ENSRNOG00000019701

Protein

Protein identifiers

Uncharacterized protein C11orf98 — E9PRG8 (reviewed: E9PRG8)

All UniProt accessions (2): E9PRG8, A0A494BXY3

RefSeq proteins (1): NP_001273015* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037691	C11orf98	Family

Pfam: PF17719

UniProt features (3 total): region of interest 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8INF	ELECTRON MICROSCOPY	3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-E9PRG8-F1	76.82	0.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, BRUINS_UVC_RESPONSE_LATE, ARID5B_TARGET_GENES, CHAF1B_TARGET_GENES, CREB3L4_TARGET_GENES, GTF2E2_TARGET_GENES, HOXB4_TARGET_GENES, NFE2L1_TARGET_GENES, NKX2_3_TARGET_GENES, PSMB5_TARGET_GENES, SETD7_TARGET_GENES, SRSF9_TARGET_GENES, TOP2B_TARGET_GENES, ZNF282_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

246 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C11orf98	NUCLEOLIN	P19338	554
C11orf98	ARHGAP40	Q5TG30	507
C11orf98	OVCA2	Q8WZ82	447
C11orf98	LIN7B	Q9HAP6	371
C11orf98	PRDM11	Q9NQV5	370
C11orf98	NEURL1B	A8MQ27	353
C11orf98	VPS13D	Q5THJ4	348
C11orf98	NBDY	A0A0U1RRE5	322
C11orf98	NDUFA7	O95182	305
C11orf98	LRRC10B	A6NIK2	288
C11orf98	DENND10	Q8TCE6	275
C11orf98	PZP	P20742	270
C11orf98	AATF	Q9NY61	269
C11orf98	CXorf38	Q8TB03	266
C11orf98	XRCC5	P13010	264

IntAct

50 interactions, top by confidence:

A	B	Type	Score
N	RBM47	psi-mi:“MI:0914”(association)	0.530
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
GSK3A	C11orf98	psi-mi:“MI:0915”(physical association)	0.370
GSK3B	C11orf98	psi-mi:“MI:0915”(physical association)	0.370
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350
OAS3	PTBP1	psi-mi:“MI:0914”(association)	0.350
SCARB2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
DIPK2A	C11orf98	psi-mi:“MI:0914”(association)	0.350
SLC16A11	PABPC4	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
IPO5	C11orf98	psi-mi:“MI:0914”(association)	0.350
PSME3	C11orf98	psi-mi:“MI:0914”(association)	0.350
RPL19	RPS3A	psi-mi:“MI:0914”(association)	0.350
RPL5	RPS3A	psi-mi:“MI:0914”(association)	0.350
SRP19	RPS3A	psi-mi:“MI:0914”(association)	0.350
SRP68	RPS3A	psi-mi:“MI:0914”(association)	0.350
SRP72	RPS3A	psi-mi:“MI:0914”(association)	0.350
MACROH2A2	ZNF316	psi-mi:“MI:0914”(association)	0.350
SF3B1	RBM10	psi-mi:“MI:0914”(association)	0.350
SF3B1	FAM83G	psi-mi:“MI:0914”(association)	0.350
GATA2	ILVBL	psi-mi:“MI:0914”(association)	0.350
CTNNA1	MYO1G	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A1CM73, A1DLV0, A2R4J9, A3GHA4, A3LVY7, A4RA36, A5DBJ8, A5DFI4, A5DZY1, A6RF09, A6RJP7, A6ZV63, A6ZVE9, A7A239, A7E564, A7TKU9, B3LTX4, B5VKI1, C4Y2M6, C5DMI3, C5DP87, C7GWJ7, E9PRG8, P36080, P43586, P53251, Q0CH56, Q0V2R4, Q1E403, Q28IC1, Q2U9C6, Q2V2Q1, Q4WDG1, Q5AJF1, Q5AYS4, Q6BRC6, Q6C8H2, Q6CLA4, Q6CN59, Q6CN96

Diamond homologs: E9PRG8, Q9D937

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 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
SRP-dependent cotranslational protein targeting to membrane	7	18.0×	3e-05
Response of EIF2AK4 (GCN2) to amino acid deficiency	5	14.2×	4e-03
Major pathway of rRNA processing in the nucleolus and cytosol	6	9.5×	4e-03
Translation	5	8.0×	1e-02

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	5	18.9×	1e-03
translation	6	12.6×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

524 predictions. Top by Δscore:

Variant	Effect	Δscore
11:62663232:TCA:T	donor_loss	1.0000
11:62663234:A:T	donor_loss	1.0000
11:62663235:C:A	donor_loss	1.0000
11:62663238:T:A	donor_gain	1.0000
11:62663329:TGGAC:T	acceptor_gain	1.0000
11:62663331:GAC:G	acceptor_gain	1.0000
11:62663332:AC:A	acceptor_gain	1.0000
11:62663333:CC:C	acceptor_gain	1.0000
11:62663333:CCTGA:C	acceptor_gain	1.0000
11:62663334:C:CA	acceptor_loss	1.0000
11:62663334:C:CC	acceptor_gain	1.0000
11:62663334:C:CG	acceptor_loss	1.0000
11:62663337:A:AC	acceptor_gain	1.0000
11:62663341:G:C	acceptor_gain	1.0000
11:62663341:G:GC	acceptor_gain	1.0000
11:62663345:G:C	acceptor_gain	1.0000
11:62663345:G:GC	acceptor_gain	1.0000
11:62664843:A:AC	donor_gain	1.0000
11:62664844:C:CC	donor_gain	1.0000
11:62664846:TA:T	donor_loss	1.0000
11:62664846:TACG:T	donor_loss	1.0000
11:62664847:A:AC	donor_gain	1.0000
11:62664847:ACG:A	donor_gain	1.0000
11:62664847:ACGC:A	donor_gain	1.0000
11:62664847:ACGCC:A	donor_gain	1.0000
11:62664848:C:CA	donor_gain	1.0000
11:62664848:CG:C	donor_gain	1.0000
11:62664848:CGC:C	donor_gain	1.0000
11:62664848:CGCC:C	donor_gain	1.0000
11:62664848:CGCCC:C	donor_gain	1.0000

AlphaMissense

786 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:62663297:C:A	K67N	0.993
11:62663297:C:G	K67N	0.993
11:62663307:A:T	L64Q	0.993
11:62663315:G:C	N61K	0.992
11:62663315:G:T	N61K	0.992
11:62663301:C:T	G66E	0.991
11:62663313:A:T	I62N	0.991
11:62663327:A:C	S57R	0.991
11:62663327:A:T	S57R	0.991
11:62663329:T:G	S57R	0.991
11:62663313:A:C	I62S	0.990
11:62664950:T:A	K21N	0.990
11:62664950:T:G	K21N	0.990
11:62663294:C:A	K68N	0.989
11:62663294:C:G	K68N	0.989
11:62663285:T:A	K71N	0.988
11:62663285:T:G	K71N	0.988
11:62663301:C:A	G66V	0.988
11:62663313:A:G	I62T	0.988
11:62664900:C:T	G38E	0.988
11:62663298:T:A	K67M	0.987
11:62664854:C:A	K53N	0.987
11:62664854:C:G	K53N	0.987
11:62664861:A:G	L51P	0.986
11:62664901:C:A	G38W	0.986
11:62663299:T:G	K67Q	0.983
11:62663296:T:C	K68E	0.982
11:62663298:T:G	K67T	0.982
11:62663299:T:C	K67E	0.982
11:62665143:G:C	N9K	0.982

dbSNP variants (sampled 300 via entrez): RS1001041985 (11:62662455 T>C), RS1003009191 (11:62665794 C>A,T), RS1003195972 (11:62664525 T>C), RS1003659267 (11:62664236 T>C), RS1005090602 (11:62666935 G>A), RS1005348888 (11:62666518 C>T), RS1005510640 (11:62663454 C>G,T), RS1006581488 (11:62666118 C>A,G,T), RS1007577564 (11:62665300 G>A,T), RS1007809209 (11:62663859 G>A,C), RS1008434892 (11:62665083 G>A), RS1008529247 (11:62664390 G>C), RS1008581701 (11:62663868 T>C,G), RS1008867839 (11:62664809 T>C), RS1009560190 (11:62662473 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
methylmercuric chloride	increases expression	1
benzo(e)pyrene	decreases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
LDN 193189	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ivermectin	decreases expression	1
Methapyrilene	decreases methylation	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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