C11orf24

Summary

C11orf24 (chromosome 11 open reading frame 24, HGNC:1174) is a protein-coding gene on chromosome 11q13.2, encoding Uncharacterized protein C11orf24 (Q96F05).

Located in Golgi apparatus and nucleoplasm.

Source: NCBI Gene 53838 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 13 total — 1 pathogenic
• MANE Select transcript: NM_022338

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1174
Approved symbol	C11orf24
Name	chromosome 11 open reading frame 24
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	DM4E3
Ensembl gene	ENSG00000171067
Ensembl biotype	protein_coding
OMIM	610880
Entrez	53838

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 5 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000304271, ENST00000527280, ENST00000529339, ENST00000529590, ENST00000530166, ENST00000531745, ENST00000532534, ENST00000532969, ENST00000533310, ENST00000853014, ENST00000853015, ENST00000853016, ENST00000853017, ENST00000853019, ENST00000853021, ENST00000919032, ENST00000945965

RefSeq mRNA: 2 — MANE Select: NM_022338 NM_001300913, NM_022338

CCDS: CCDS73338, CCDS8180

Canonical transcript exons

ENST00000304271 — 4 exons

Exon	Start	End
ENSE00001166587	68268054	68268251
ENSE00001261746	68261338	68262918
ENSE00002183518	68271857	68271973
ENSE00003800060	68263692	68263866

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 96.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.7079 / max 251.5144, expressed in 1810 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120994	35.1291	1810
120995	2.5788	1381

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	96.77	gold quality
stromal cell of endometrium	CL:0002255	95.54	gold quality
ascending aorta	UBERON:0001496	94.57	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.47	gold quality
thoracic aorta	UBERON:0001515	94.45	gold quality
mucosa of transverse colon	UBERON:0004991	94.30	gold quality
peripheral nervous system	UBERON:0000010	93.89	gold quality
nerve	UBERON:0001021	93.89	gold quality
tibial nerve	UBERON:0001323	93.89	gold quality
right coronary artery	UBERON:0001625	93.72	gold quality
small intestine	UBERON:0002108	93.64	gold quality
left coronary artery	UBERON:0001626	93.27	gold quality
aorta	UBERON:0000947	93.01	gold quality
jejunal mucosa	UBERON:0000399	92.59	gold quality
duodenum	UBERON:0002114	92.52	gold quality
coronary artery	UBERON:0001621	92.42	gold quality
ileal mucosa	UBERON:0000331	92.29	gold quality
descending thoracic aorta	UBERON:0002345	92.29	gold quality
transverse colon	UBERON:0001157	92.21	gold quality
tibial artery	UBERON:0007610	92.08	gold quality
popliteal artery	UBERON:0002250	92.07	gold quality
body of uterus	UBERON:0009853	91.74	gold quality
left uterine tube	UBERON:0001303	91.48	gold quality
minor salivary gland	UBERON:0001830	91.36	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.18	gold quality
right atrium auricular region	UBERON:0006631	91.16	gold quality
granulocyte	CL:0000094	90.87	gold quality
body of stomach	UBERON:0001161	90.70	gold quality
liver	UBERON:0002107	90.69	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	90.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	18.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting C11orf24, 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-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-6848-3P	99.64	66.49	885
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-6843-3P	99.26	66.42	915
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-6852-5P	99.17	66.69	2073

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000089303
mus_musculus	1810055G02Rik	ENSMUSG00000035372
rattus_norvegicus	C1h11orf24	ENSRNOG00000025245

Paralogs (2): MANSC1 (ENSG00000111261), MANSC4 (ENSG00000205693)

Protein

Protein identifiers

Uncharacterized protein C11orf24 — Q96F05 (reviewed: Q96F05)

Alternative names: Protein DM4E3

All UniProt accessions (3): E9PI63, E9PRU5, Q96F05

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane. Golgi apparatus. trans-Golgi network membrane.

Tissue specificity. Highest expression in heart, placenta, liver, pancreas and colon. Also detected in brain, lung, skeletal muscle, kidney, spleen, prostate, testis, ovary and small intestine. Lowest expression in thymus and leukocytes.

RefSeq proteins (2): NP_001287842, NP_071733* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR041056	DUF5585	Family
IPR052660	Erythrocyte_Invasion_ImmMod	Family

Pfam: PF17823

UniProt features (15 total): compositionally biased region 4, region of interest 3, sequence variant 2, topological domain 2, signal peptide 1, chain 1, glycosylation site 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96F05-F1	52.28	0.05

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 142 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, chr11q13, SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE, WEI_MYCN_TARGETS_WITH_E_BOX, ROSS_LEUKEMIA_WITH_MLL_FUSIONS, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, AFP1_Q6, TIEN_INTESTINE_PROBIOTICS_24HR_UP, SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL, BASAKI_YBX1_TARGETS_UP, DOUGLAS_BMI1_TARGETS_UP, SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM, NUYTTEN_EZH2_TARGETS_DN, MGGAAGTG_GABP_B

GO Biological Process (0):

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

GO Cellular Component (4): nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
nuclear lumen	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C11orf24	SMIM13	P0DJ93	479
C11orf24	ZNF616	Q08AN1	432
C11orf24	CDC14B	O60729	396
C11orf24	VMA22	Q96NT0	373
C11orf24	RCCD1	A6NED2	371
C11orf24	TMEM109	Q9BVC6	368
C11orf24	TMED9	Q9BVK6	343
C11orf24	CREBL2	O60519	320
C11orf24	CALHM6	Q5R3K3	311
C11orf24	KPNA5	O15131	304
C11orf24	ZNF367	Q7RTV3	300
C11orf24	ZNF79	Q15937	292
C11orf24	TMED3	Q9Y3Q3	290
C11orf24	CNIH4	Q9P003	289
C11orf24	TGOLN2	O43493	287

IntAct

28 interactions, top by confidence:

A	B	Type	Score
CREB3L1	C11orf24	psi-mi:“MI:0915”(physical association)	0.560
FAM209A	C11orf24	psi-mi:“MI:0915”(physical association)	0.560
SSMEM1	C11orf24	psi-mi:“MI:0915”(physical association)	0.560
MGST3	C11orf24	psi-mi:“MI:0915”(physical association)	0.560
FFAR2	C11orf24	psi-mi:“MI:0915”(physical association)	0.560
C11orf24	TMEM80	psi-mi:“MI:0915”(physical association)	0.560
SLC10A6	C11orf24	psi-mi:“MI:0915”(physical association)	0.560
C11orf24	NME2P1	psi-mi:“MI:0914”(association)	0.530
MEP1B	C11orf24	psi-mi:“MI:0915”(physical association)	0.370
	TMEM223	psi-mi:“MI:0914”(association)	0.350
C11orf24	CREB3L1	psi-mi:“MI:0915”(physical association)	0.000
C11orf24	FAM209A	psi-mi:“MI:0915”(physical association)	0.000
C11orf24	SSMEM1	psi-mi:“MI:0915”(physical association)	0.000
C11orf24	MGST3	psi-mi:“MI:0915”(physical association)	0.000
C11orf24	FFAR2	psi-mi:“MI:0915”(physical association)	0.000
C11orf24	TMEM80	psi-mi:“MI:0915”(physical association)	0.000
C11orf24	SLC10A6	psi-mi:“MI:0915”(physical association)	0.000
spoIIIAE	C11orf24	psi-mi:“MI:0915”(physical association)	0.000
corE	C11orf24	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): VAT1L (Affinity Capture-MS), RNF166 (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), VWA1 (Affinity Capture-MS), C11orf24 (Two-hybrid), C11orf24 (Affinity Capture-MS), C11orf24 (Affinity Capture-RNA), C11orf24 (Two-hybrid), C11orf24 (Two-hybrid), C11orf24 (Two-hybrid), C11orf24 (Two-hybrid), C11orf24 (Two-hybrid), C11orf24 (Two-hybrid), TMEM80 (Two-hybrid), C11orf24 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUW6, A1EGX6, A6NM11, A6NMS7, A6QLF8, D3YU32, I3L273, J3KML8, O35930, O60309, Q08DY0, Q14242, Q2TBI7, Q32KG4, Q32L62, Q3MIW9, Q3TNW5, Q3V0E1, Q4R729, Q5VWK0, Q5VYM1, Q62170, Q659K0, Q68DN1, Q6AZ54, Q6MG22, Q6UXB8, Q6ZRG5, Q8BUE7, Q8K4E0, Q8N307, Q8N3K9, Q8TCU4, Q8WNU4, Q8WXI7, Q95JY5, Q96F05, Q96JA4, Q96M34, Q96M43

Diamond homologs: Q4V7A5, Q96F05, Q9D8N1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2685409	GRCh37/hg19 11q13.2(chr11:67799161-68393180)x1	Pathogenic

SpliceAI

718 predictions. Top by Δscore:

Variant	Effect	Δscore
11:68262920:T:C	acceptor_gain	1.0000
11:68262919:C:CC	acceptor_gain	0.9900
11:68262927:C:CT	acceptor_gain	0.9900
11:68262928:A:T	acceptor_gain	0.9900
11:68263690:A:AC	donor_gain	0.9900
11:68263691:C:CC	donor_gain	0.9900
11:68264749:AGTG:A	donor_gain	0.9900
11:68270822:AAT:A	donor_gain	0.9900
11:68271852:CTTA:C	donor_loss	0.9900
11:68271853:TTA:T	donor_loss	0.9900
11:68271854:TA:T	donor_loss	0.9900
11:68271855:A:AC	donor_gain	0.9900
11:68271855:AC:A	donor_gain	0.9900
11:68271856:C:CC	donor_gain	0.9900
11:68271856:C:CT	donor_loss	0.9900
11:68271856:CC:C	donor_gain	0.9900
11:68262918:CCT:C	acceptor_gain	0.9800
11:68263560:C:A	donor_gain	0.9800
11:68262916:TGCC:T	acceptor_loss	0.9700
11:68262917:GCCT:G	acceptor_loss	0.9700
11:68262920:T:TC	acceptor_gain	0.9700
11:68263864:GATCT:G	acceptor_loss	0.9700
11:68263867:C:CC	acceptor_gain	0.9700
11:68263867:C:CG	acceptor_loss	0.9700
11:68263868:T:A	acceptor_loss	0.9700
11:68264745:A:AC	donor_gain	0.9600
11:68264746:C:CC	donor_gain	0.9600
11:68268247:CGCAT:C	acceptor_gain	0.9600
11:68268278:CCTTA:C	acceptor_gain	0.9600
11:68268259:T:C	acceptor_gain	0.9500

AlphaMissense

2899 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:68261676:A:G	I440T	0.998
11:68261679:A:G	L439S	0.998
11:68261676:A:C	I440S	0.997
11:68261676:A:T	I440N	0.997
11:68261685:T:A	D437V	0.995
11:68261667:A:G	M443T	0.994
11:68261686:C:G	D437H	0.992
11:68261664:T:C	Y444C	0.991
11:68261666:C:A	M443I	0.991
11:68261666:C:G	M443I	0.991
11:68261666:C:T	M443I	0.991
11:68261671:C:A	G442W	0.991
11:68261770:C:G	G409R	0.990
11:68261770:C:T	G409R	0.990
11:68261672:G:C	N441K	0.989
11:68261672:G:T	N441K	0.989
11:68261673:T:A	N441I	0.989
11:68261685:T:G	D437A	0.989
11:68261670:C:A	G442V	0.988
11:68261684:G:C	D437E	0.987
11:68261684:G:T	D437E	0.987
11:68261685:T:C	D437G	0.984
11:68263764:A:G	W2R	0.984
11:68263764:A:T	W2R	0.984
11:68261665:A:G	Y444H	0.982
11:68261725:C:G	A424P	0.982
11:68261671:C:G	G442R	0.981
11:68261671:C:T	G442R	0.981
11:68261682:T:C	Y438C	0.980
11:68261708:C:A	K429N	0.979

dbSNP variants (sampled 300 via entrez): RS1000204076 (11:68263424 T>C), RS1000210054 (11:68271926 G>C), RS1000236321 (11:68271993 G>A), RS1000391853 (11:68266233 G>A), RS1000764592 (11:68265958 T>A), RS1000984643 (11:68268487 C>T), RS1001249965 (11:68268767 C>T), RS1001347651 (11:68269167 C>T), RS1001353390 (11:68268191 T>C), RS1001481613 (11:68268870 T>A,C), RS1001582217 (11:68266686 G>A), RS1002213942 (11:68260880 T>C), RS1002429030 (11:68270787 T>C), RS1002870303 (11:68271224 C>T), RS1002994066 (11:68265743 C>A,T)

Disease associations

OMIM: gene MIM:610880 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006624_6	Systolic blood pressure	2.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, increases expression, affects expression	4
bisphenol A	affects expression, affects cotreatment, increases methylation, decreases expression	3
Tetrachlorodibenzodioxin	increases expression	2
Cadmium Chloride	increases abundance, decreases expression	2
GSK-J4	decreases expression	1
lead acetate	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
cupric chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
Rosiglitazone	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases expression	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	increases expression	1
Estradiol	increases expression	1
Fluorouracil	affects response to substance	1
Lead	decreases expression	1
Smoke	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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