C11orf21

Summary

C11orf21 (chromosome 11 open reading frame 21, HGNC:13231) is a protein-coding gene on chromosome 11p15.5, encoding Uncharacterized protein C11orf21 (Q9P2W6).

Predicted to be located in cytoplasm.

Source: NCBI Gene 29125 — RefSeq curated summary.

At a glance

• GWAS associations: 21
• Clinical variants (ClinVar): 25 total — 1 pathogenic
• MANE Select transcript: NM_001329958

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13231
Approved symbol	C11orf21
Name	chromosome 11 open reading frame 21
Location	11p15.5
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000110665
Ensembl biotype	protein_coding
OMIM	611033
Entrez	29125

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000381153, ENST00000456145, ENST00000470369, ENST00000495467, ENST00000856028, ENST00000856029, ENST00000856030, ENST00000856031, ENST00000856032, ENST00000961288

RefSeq mRNA: 2 — MANE Select: NM_001329958 NM_001142946, NM_001329958

CCDS: CCDS44518, CCDS86168

Canonical transcript exons

ENST00000381153 — 4 exons

Exon	Start	End
ENSE00000691475	2300520	2300613
ENSE00001487653	2295628	2297921
ENSE00001487658	2301756	2301918
ENSE00003599171	2299428	2299707

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 98.48.

FANTOM5 (CAGE): breadth broad, TPM avg 4.4269 / max 297.4962, expressed in 419 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118204	3.6681	339
118205	0.2049	97
118208	0.1272	46
118206	0.0928	52
118210	0.0815	35
118203	0.0765	28
118212	0.0583	33
118211	0.0535	27
118207	0.0462	26
118209	0.0179	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	98.48	gold quality
monocyte	CL:0000576	95.80	gold quality
mononuclear cell	CL:0000842	95.75	gold quality
leukocyte	CL:0000738	95.55	gold quality
blood	UBERON:0000178	92.79	gold quality
trabecular bone tissue	UBERON:0002483	89.54	gold quality
bone marrow	UBERON:0002371	89.18	gold quality
apex of heart	UBERON:0002098	88.65	gold quality
bone marrow cell	CL:0002092	88.45	gold quality
heart left ventricle	UBERON:0002084	87.19	gold quality
cardiac ventricle	UBERON:0002082	86.72	gold quality
spleen	UBERON:0002106	83.50	gold quality
right atrium auricular region	UBERON:0006631	81.11	gold quality
heart	UBERON:0000948	80.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.57	silver quality
cardiac atrium	UBERON:0002081	80.10	gold quality
lymph node	UBERON:0000029	79.03	gold quality
vermiform appendix	UBERON:0001154	77.39	gold quality
myocardium	UBERON:0002349	75.01	silver quality
right lung	UBERON:0002167	74.38	gold quality
upper lobe of left lung	UBERON:0008952	73.93	gold quality
caecum	UBERON:0001153	72.46	gold quality
upper lobe of lung	UBERON:0008948	72.34	gold quality
gall bladder	UBERON:0002110	71.10	gold quality
left ventricle myocardium	UBERON:0006566	69.98	silver quality
cardiac muscle of right atrium	UBERON:0003379	69.37	silver quality
body of stomach	UBERON:0001161	69.36	gold quality
periodontal ligament	UBERON:0008266	69.04	silver quality
colonic epithelium	UBERON:0000397	67.82	gold quality
lung	UBERON:0002048	66.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

50 targeting C11orf21, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-609	99.82	64.26	505
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-4727-5P	99.23	67.55	1154
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-1257	98.97	68.02	1133
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-6794-3P	98.76	66.99	894
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-138-5P	98.43	70.49	1292
HSA-MIR-6780A-3P	98.42	67.49	1518
HSA-MIR-6784-3P	98.39	64.88	662

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Uncharacterized protein C11orf21 — Q9P2W6 (reviewed: Q9P2W6)

All UniProt accessions (2): Q9P2W6, E9PAM5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expressed exclusively in heart.

RefSeq proteins (2): NP_001136418, NP_001316887* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027894	DUF4620	Family

Pfam: PF15399

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2W6-F1	55.54	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 109 (showing top): GNF2_CASP8, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, HOEBEKE_LYMPHOID_STEM_CELL_UP, GNF2_PTPRC, MULLIGHAN_MLL_SIGNATURE_1_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, MARTENS_BOUND_BY_PML_RARA_FUSION, ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP, VALK_AML_CLUSTER_13, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, E2F5_TARGET_GENES, NFKBIA_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

238 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C11orf21	TSPAN32	Q96QS1	720
C11orf21	OR2L13	Q8N349	583
C11orf21	ZNF888	P0CJ79	543
C11orf21	ACOXL	Q9NUZ1	447
C11orf21	ZFP57	Q9NU63	397
C11orf21	TSSC4	Q9Y5U2	365
C11orf21	ODF1	Q14990	352
C11orf21	CRACDL	Q6NV74	348
C11orf21	ZNF549	Q6P9A3	322
C11orf21	LMAN1L	Q9HAT1	317
C11orf21	ZNF418	Q8TF45	316
C11orf21	R3HCC1	Q9Y3T6	311
C11orf21	CCDC85C	A6NKD9	311
C11orf21	KRTCAP3	Q53RY4	309
C11orf21	MOB3A	Q96BX8	301

IntAct

0 interactions, top by confidence:

BioGRID (1): C11orf21 (Positive Genetic)

ESM2 similar proteins: A0A1B0GUV1, A0A1B0GVM6, A0A3B3IS91, A0A455ZAR2, A0A6I8MX38, A0A6I8PU40, A5CVC4, C0HLZ6, D3DTV9, I3L0S3, L7N648, O70738, O83165, O90299, P03289, P11300, P12064, P16807, P16814, P16838, P25133, P28964, P29164, P69616, P69617, P89476, Q04221, Q04612, Q2J4A0, Q5JLA7, Q5R4B0, Q64364, Q6IPW1, Q6ZSA8, Q81870, Q86625, Q8N1X5, Q8N726, Q8N7S6, Q8N9T2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	17
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
147689	GRCh38/hg38 11p15.5-15.4(chr11:1537379-3360769)x3	Pathogenic

SpliceAI

219 predictions. Top by Δscore:

Variant	Effect	Δscore
11:2302954:ATGGG:A	donor_gain	1.0000
11:2302956:GGG:G	donor_gain	1.0000
11:2302957:GG:G	donor_gain	1.0000
11:2302957:GGG:G	donor_gain	1.0000
11:2302958:GG:G	donor_gain	1.0000
11:2302959:G:GG	donor_gain	1.0000
11:2302842:A:AG	acceptor_gain	0.9900
11:2302843:G:GG	acceptor_gain	0.9900
11:2302843:GCT:G	acceptor_gain	0.9900
11:2302955:TGGG:T	donor_gain	0.9900
11:2302956:GGGG:G	donor_gain	0.9900
11:2302066:G:GG	donor_gain	0.9800
11:2302108:G:GT	donor_gain	0.9800
11:2302109:G:T	donor_gain	0.9700
11:2302838:CCACA:C	acceptor_loss	0.9700
11:2302839:CACA:C	acceptor_loss	0.9700
11:2302840:ACAGC:A	acceptor_loss	0.9700
11:2302841:CAGC:C	acceptor_loss	0.9700
11:2302843:G:A	acceptor_loss	0.9700
11:2302447:GCC:G	donor_gain	0.9600
11:2302065:A:AG	donor_gain	0.9500
11:2302837:T:G	acceptor_loss	0.9500
11:2302842:AGCT:A	acceptor_gain	0.9500
11:2302843:GCTG:G	acceptor_gain	0.9500
11:2302748:G:GT	donor_gain	0.9300
11:2302061:GGGCA:G	donor_gain	0.9200
11:2302062:GGCAG:G	donor_gain	0.9200
11:2302076:GTC:G	donor_gain	0.9100
11:2302077:TCT:T	donor_gain	0.9100
11:2302062:GGCA:G	donor_gain	0.9000

AlphaMissense

837 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:2299474:C:A	W127C	0.901
11:2299474:C:G	W127C	0.901
11:2299476:A:G	W127R	0.862
11:2299476:A:T	W127R	0.862
11:2300598:C:A	W23C	0.843
11:2300598:C:G	W23C	0.843
11:2299547:A:G	I103T	0.833
11:2300600:A:G	W23R	0.792
11:2300600:A:T	W23R	0.792
11:2299475:C:A	W127L	0.779
11:2299547:A:T	I103N	0.779
11:2299573:A:C	S94R	0.757
11:2299573:A:T	S94R	0.757
11:2299575:T:G	S94R	0.757
11:2299534:C:A	W107C	0.726
11:2299534:C:G	W107C	0.726
11:2299547:A:C	I103S	0.724
11:2299475:C:G	W127S	0.715
11:2299597:C:A	W86C	0.688
11:2299597:C:G	W86C	0.688
11:2299559:A:G	L99S	0.661
11:2300553:C:A	W38C	0.627
11:2300553:C:G	W38C	0.627
11:2299539:C:G	G106R	0.616
11:2299539:C:T	G106R	0.616
11:2299590:A:G	C89R	0.616
11:2299478:C:A	R126M	0.612
11:2299536:A:G	W107R	0.607
11:2299536:A:T	W107R	0.607
11:2300599:C:A	W23L	0.602

dbSNP variants (sampled 300 via entrez): RS1000135988 (11:2299008 G>A), RS1000271975 (11:2298835 G>A), RS1000318598 (11:2304502 T>G), RS1000503694 (11:2300430 TG>T), RS1000598029 (11:2299882 G>A), RS1001164130 (11:2295195 A>G), RS1001898320 (11:2296575 G>T), RS1002228841 (11:2296138 T>C), RS1002646183 (11:2298745 G>C), RS1002677466 (11:2298559 C>T), RS1002825660 (11:2303237 C>A,T), RS1002836093 (11:2304174 C>A,T), RS1003095133 (11:2297437 C>T), RS1003168147 (11:2297691 G>A), RS1003265579 (11:2303052 T>C,G)

Disease associations

OMIM: gene MIM:611033 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST001762_619	Obesity-related traits	5.000000e-06
GCST002299_14	Chronic lymphocytic leukemia	3.000000e-06
GCST003468_12	Chronic lymphocytic leukemia	4.000000e-08
GCST004146_15	Chronic lymphocytic leukemia	5.000000e-11
GCST004602_189	Mean corpuscular volume	6.000000e-12
GCST004618_33	White blood cell count (basophil)	1.000000e-13
GCST004624_185	Sum eosinophil basophil counts	4.000000e-09
GCST004630_244	Mean corpuscular hemoglobin	2.000000e-12
GCST004631_52	Basophil percentage of white cells	2.000000e-12
GCST005024_37	Pursuit maintenance gain	3.000000e-07
GCST005028_1	Pursuit maintenance gain in psychotic disorders	2.000000e-08
GCST010725_20	Malaria	4.000000e-69
GCST010725_33	Malaria	2.000000e-67
GCST010725_51	Malaria	1.000000e-55
GCST012277_3	Clostridioides difficle infection	3.000000e-07
GCST90002381_293	Eosinophil count	8.000000e-14
GCST90002390_501	Mean corpuscular hemoglobin	1.000000e-30
GCST90002392_554	Mean corpuscular volume	2.000000e-26
GCST90002393_347	Monocyte count	2.000000e-16
GCST90002397_556	Mean spheric corpuscular volume	6.000000e-20
GCST90002403_237	Red blood cell count	7.000000e-18

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0005106	body composition measurement
EFO:0005090	basophil count
EFO:0004842	eosinophil count
EFO:0004527	mean corpuscular hemoglobin
EFO:0007992	basophil percentage of leukocytes
EFO:0008433	pursuit maintenance gain measurement
EFO:0009130	clostridium difficile infection
EFO:0005091	monocyte count
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
beauvericin	affects cotreatment, decreases expression	1
bisphenol A	decreases methylation	1
beta-lapachone	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
enniatins	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Copper	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Nickel	increases expression	1
Triclosan	decreases expression	1
Valproic Acid	increases methylation	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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