C11orf16

Summary

C11orf16 (chromosome 11 open reading frame 16, HGNC:1169) is a protein-coding gene on chromosome 11p15.4, encoding Uncharacterized protein C11orf16 (Q9NQ32).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_020643

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1169
Approved symbol	C11orf16
Name	chromosome 11 open reading frame 16
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000176029
Ensembl biotype	protein_coding
Entrez	56673

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 2 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000326053, ENST00000525780, ENST00000526227, ENST00000527607, ENST00000528830, ENST00000528998

RefSeq mRNA: 1 — MANE Select: NM_020643 NM_020643

CCDS: CCDS7794

Canonical transcript exons

ENST00000326053 — 7 exons

Exon	Start	End
ENSE00001103119	8926940	8927174
ENSE00001268265	8929377	8929533
ENSE00001268282	8925463	8926107
ENSE00001268329	8921294	8921515
ENSE00002154618	8932901	8932947
ENSE00003625661	8920076	8920450
ENSE00003666523	8932142	8932326

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 96.62.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0306 / max 5.9936, expressed in 18 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118529	0.0260	16
118528	0.0046	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelium of bronchus	UBERON:0002031	96.62	gold quality
bronchial epithelial cell	CL:0002328	96.50	gold quality
bronchus	UBERON:0002185	96.41	gold quality
right uterine tube	UBERON:0001302	95.71	gold quality
type B pancreatic cell	CL:0000169	95.25	gold quality
olfactory bulb	UBERON:0002264	95.08	gold quality
diaphragm	UBERON:0001103	93.83	gold quality
vena cava	UBERON:0004087	91.81	silver quality
nasal cavity epithelium	UBERON:0005384	91.39	gold quality
trachea	UBERON:0003126	90.55	gold quality
cardia of stomach	UBERON:0001162	89.92	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.74	gold quality
epithelium of nasopharynx	UBERON:0001951	89.72	gold quality
mucosa of paranasal sinus	UBERON:0005030	89.34	gold quality
tongue squamous epithelium	UBERON:0006919	88.68	silver quality
subthalamic nucleus	UBERON:0001906	88.65	silver quality
thymus	UBERON:0002370	88.33	silver quality
ventral tegmental area	UBERON:0002691	88.30	silver quality
cervix squamous epithelium	UBERON:0006922	88.03	gold quality
dorsal plus ventral thalamus	UBERON:0001897	87.99	silver quality
cardiac muscle of right atrium	UBERON:0003379	87.29	gold quality
tongue	UBERON:0001723	87.27	silver quality
cerebellar vermis	UBERON:0004720	87.21	gold quality
pharyngeal mucosa	UBERON:0000355	86.81	silver quality
pons	UBERON:0000988	86.65	gold quality
lateral globus pallidus	UBERON:0002476	86.33	silver quality
superior surface of tongue	UBERON:0007371	86.28	silver quality
inferior vagus X ganglion	UBERON:0005363	86.27	silver quality
pylorus	UBERON:0001166	86.13	gold quality
superior vestibular nucleus	UBERON:0007227	86.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting C11orf16, 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-153-5P	99.89	73.86	6317
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-4687-5P	99.14	66.26	488
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-4691-3P	98.11	66.83	1204
HSA-MIR-6893-3P	97.79	64.91	1238
HSA-MIR-4456	97.50	64.88	1678
HSA-MIR-6791-3P	97.45	64.31	1123
HSA-MIR-6829-3P	97.45	64.31	1137
HSA-MIR-645	97.28	66.30	486
HSA-MIR-370-3P	97.09	64.92	1221
HSA-MIR-668-3P	96.18	65.80	673

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-8l13.5	ENSDARG00000101630
mus_musculus	BC051019	ENSMUSG00000031022
rattus_norvegicus	C1h11orf16	ENSRNOG00000013713

Protein

Protein identifiers

Uncharacterized protein C11orf16 — Q9NQ32 (reviewed: Q9NQ32)

All UniProt accessions (2): Q9NQ32, E9PNY9

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NQ32-1	1	yes
Q9NQ32-2	2

RefSeq proteins (1): NP_065694* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032770	DUF4537	Domain

Pfam: PF15057

UniProt features (11 total): sequence conflict 5, sequence variant 2, chain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQ32-F1	52.18	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): MYB_Q3, MYB_Q5_01, DODD_NASOPHARYNGEAL_CARCINOMA_DN, PTEN_DN.V1_UP, KRAS.AMP.LUNG_UP.V1_UP, MIR153_5P, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, GSE13229_IMM_VS_INTMATURE_NKCELL_UP, MIR668_3P, GSE13485_CTRL_VS_DAY1_YF17D_VACCINE_PBMC_DN, GSE13485_DAY1_VS_DAY3_YF17D_VACCINE_PBMC_UP, GSE14308_NAIVE_CD4_TCELL_VS_INDUCED_TREG_DN, TGACAGNY_MEIS1_01, GAO_ESOPHAGUS_25W_C1_CILIATED_EPITHELIAL_CELLS, GSE17721_PAM3CSK4_VS_GADIQUIMOD_16H_BMDC_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

290 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C11orf16	PWWP2A	Q96N64	678
C11orf16	C12orf56	Q8IXR9	623
C11orf16	C6orf136	Q5SQH8	542
C11orf16	KIAA0930	Q6ICG6	507
C11orf16	C11orf42	Q8N5U0	447
C11orf16	TUBA4B	Q9H853	431
C11orf16	TTC8	Q8TAM2	417
C11orf16	SF3B4	Q15427	373
C11orf16	POLG2	Q9UHN1	365
C11orf16	UPF3A	Q9H1J1	347
C11orf16	ITM2B	Q9Y287	324
C11orf16	MAGED2	Q9UNF1	322
C11orf16	CORO1C	Q9ULV4	313
C11orf16	CCT4	P50991	306
C11orf16	RPLP1	P05386	301

IntAct

3 interactions, top by confidence:

A	B	Type	Score
EWSR1	C11orf16	psi-mi:“MI:0915”(physical association)	0.370
SMYD1	C11orf16	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (17): C11orf16 (Two-hybrid), C11orf16 (Biochemical Activity), C11orf16 (Two-hybrid), C11orf16 (Two-hybrid), KRTAP8-1 (Two-hybrid), KRTAP6-1 (Two-hybrid), KRTAP19-6 (Two-hybrid), KRTAP19-2 (Two-hybrid), KRTAP19-5 (Two-hybrid), CYSRT1 (Two-hybrid), KRTAP19-7 (Two-hybrid), KRTAP7-1 (Two-hybrid), C11orf16 (Affinity Capture-MS), C11orf16 (Cross-Linking-MS (XL-MS)), C11orf16 (Affinity Capture-MS)

ESM2 similar proteins: A0A5F9ZHS7, A1YGK1, A2T7E6, A8MZG2, O08574, O43593, O60393, O75593, O88621, O95231, P0C1T1, P0CG20, P20428, P97609, Q04667, Q17QR5, Q2KIS6, Q2M1V0, Q2T9Q7, Q32LE6, Q497V6, Q5JUK2, Q5M844, Q5RJB0, Q5TGS1, Q61645, Q61657, Q6ZMY3, Q6ZN32, Q6ZNG2, Q7RTU1, Q8BZW2, Q8CGW9, Q8IWN7, Q8IXT2, Q8IZ20, Q8N1L9, Q8N7G0, Q8N944, Q8N9Y4

Diamond homologs: Q9JJR6, Q9NQ32

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

950 predictions. Top by Δscore:

Variant	Effect	Δscore
11:8927028:ATCC:A	donor_gain	1.0000
11:8927077:T:TA	donor_gain	1.0000
11:8929423:T:TA	donor_gain	1.0000
11:8929424:C:A	donor_gain	1.0000
11:8929531:TGC:T	acceptor_gain	1.0000
11:8929529:CATGC:C	acceptor_gain	0.9900
11:8929530:ATGC:A	acceptor_gain	0.9900
11:8929531:TGCC:T	acceptor_loss	0.9900
11:8929532:GCCTG:G	acceptor_loss	0.9900
11:8929533:CCT:C	acceptor_loss	0.9900
11:8929534:C:CC	acceptor_gain	0.9900
11:8929535:T:A	acceptor_loss	0.9900
11:8932899:AC:A	donor_gain	0.9900
11:8932900:CC:C	donor_gain	0.9900
11:8932916:C:CA	donor_gain	0.9900
11:8925973:C:CA	donor_gain	0.9800
11:8929428:T:TA	donor_gain	0.9800
11:8932897:TTA:T	donor_loss	0.9800
11:8932899:A:AT	donor_loss	0.9800
11:8932900:CCCA:C	donor_gain	0.9800
11:8921381:C:A	donor_gain	0.9700
11:8929532:GC:G	acceptor_gain	0.9700
11:8929533:CC:C	acceptor_gain	0.9700
11:8932899:A:AC	donor_gain	0.9700
11:8932900:C:CC	donor_gain	0.9700
11:8932931:AG:A	donor_gain	0.9700
11:8927175:C:CC	acceptor_gain	0.9600
11:8932923:TCC:T	donor_gain	0.9600
11:8932924:C:CT	donor_gain	0.9600
11:8932925:C:CT	donor_gain	0.9600

AlphaMissense

3012 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:8927142:G:C	F119L	0.965
11:8927142:G:T	F119L	0.965
11:8927144:A:G	F119L	0.965
11:8926083:A:T	V195D	0.958
11:8926075:A:G	W198R	0.926
11:8926075:A:T	W198R	0.926
11:8926076:G:C	F197L	0.922
11:8926076:G:T	F197L	0.922
11:8926078:A:G	F197L	0.922
11:8926077:A:G	F197S	0.916
11:8929409:A:C	Y98D	0.909
11:8926073:C:A	W198C	0.907
11:8926073:C:G	W198C	0.907
11:8929393:A:G	I103T	0.892
11:8926070:A:C	N199K	0.888
11:8926070:A:T	N199K	0.888
11:8929399:G:T	A101D	0.878
11:8927017:G:T	A161E	0.875
11:8927143:A:C	F119C	0.873
11:8926071:T:A	N199I	0.871
11:8925509:C:A	W386C	0.863
11:8925509:C:G	W386C	0.863
11:8929389:C:A	K104N	0.862
11:8929389:C:G	K104N	0.862
11:8926984:G:T	P172H	0.860
11:8926981:C:T	G173D	0.853
11:8926987:C:T	G171D	0.851
11:8929409:A:T	Y98N	0.851
11:8925511:A:G	W386R	0.849
11:8925511:A:T	W386R	0.849

dbSNP variants (sampled 300 via entrez): RS1000052672 (11:8934906 G>A,T), RS1000063773 (11:8926385 G>A), RS1000079087 (11:8920464 A>G), RS1000100418 (11:8928844 A>G), RS1000168262 (11:8929283 A>G,T), RS1000193408 (11:8932476 T>G), RS1000384086 (11:8934532 A>G,T), RS1000526128 (11:8930854 C>G), RS1000605574 (11:8924720 C>T), RS1001348249 (11:8921074 A>T), RS1001547629 (11:8920737 C>A,T), RS1001575234 (11:8926732 A>G), RS1001793178 (11:8929272 T>C), RS1001874920 (11:8919705 C>A,G,T), RS1002015079 (11:8923525 T>A,C)

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

4 associations (top):

Study	Trait	p-value
GCST005950_10	Body mass index x sex x age interaction (4df test)	6.000000e-11
GCST005951_51	Body mass index	8.000000e-11
GCST005953_4	Body mass index (age <50)	4.000000e-11
GCST010703_171	Brain morphology (MOSTest)	5.000000e-09

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Catechin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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