C16orf46

Summary

C16orf46 (chromosome 16 open reading frame 46, HGNC:26525) is a protein-coding gene on chromosome 16q23.2, encoding Uncharacterized protein C16orf46 (Q6P387).

Located in cytosol and nucleoplasm.

Source: NCBI Gene 123775 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_152337

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26525
Approved symbol	C16orf46
Name	chromosome 16 open reading frame 46
Location	16q23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32702
Ensembl gene	ENSG00000166455
Ensembl biotype	protein_coding
Entrez	123775

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000299578, ENST00000378611, ENST00000444657, ENST00000565253, ENST00000879278, ENST00000952334

RefSeq mRNA: 2 — MANE Select: NM_152337 NM_001100873, NM_152337

CCDS: CCDS10932, CCDS42201

Canonical transcript exons

ENST00000299578 — 4 exons

Exon	Start	End
ENSE00001103113	81063746	81063993
ENSE00001103120	81066193	81066281
ENSE00001478089	81077136	81077238
ENSE00001674435	81060980	81062138

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 84.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.2992 / max 71.5713, expressed in 957 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
158269	2.2992	957

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.89	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.35	silver quality
testis	UBERON:0000473	71.37	gold quality
left testis	UBERON:0004533	71.00	gold quality
right testis	UBERON:0004534	70.66	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	69.99	gold quality
right uterine tube	UBERON:0001302	69.84	gold quality
thyroid gland	UBERON:0002046	69.45	gold quality
prefrontal cortex	UBERON:0000451	69.42	gold quality
left lobe of thyroid gland	UBERON:0001120	69.24	gold quality
right lobe of thyroid gland	UBERON:0001119	69.12	gold quality
endometrium	UBERON:0001295	67.58	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.27	gold quality
frontal cortex	UBERON:0001870	67.06	gold quality
substantia nigra	UBERON:0002038	66.81	gold quality
hypothalamus	UBERON:0001898	66.76	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	66.57	gold quality
cerebral cortex	UBERON:0000956	66.22	gold quality
stromal cell of endometrium	CL:0002255	66.04	gold quality
Ammon’s horn	UBERON:0001954	65.79	gold quality
islet of Langerhans	UBERON:0000006	65.49	gold quality
amygdala	UBERON:0001876	65.34	gold quality
anterior cingulate cortex	UBERON:0009835	65.25	gold quality
temporal lobe	UBERON:0001871	65.21	gold quality
placenta	UBERON:0001987	64.61	gold quality
pituitary gland	UBERON:0000007	64.56	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	64.51	gold quality
right frontal lobe	UBERON:0002810	64.49	gold quality
brain	UBERON:0000955	64.31	gold quality
caudate nucleus	UBERON:0001873	64.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting C16orf46, 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-3613-3P	100.00	76.36	7965
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-1253	99.12	67.08	1688
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-4712-3P	98.52	65.39	822
HSA-MIR-3613-5P	98.40	68.91	604
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-647	97.73	67.79	927

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700030J22Rik	ENSMUSG00000031847
rattus_norvegicus	C19h16orf46	ENSRNOG00000045541

Protein

Protein identifiers

Uncharacterized protein C16orf46 — Q6P387 (reviewed: Q6P387)

All UniProt accessions (2): H3BQQ0, Q6P387

Isoforms (2)

UniProt ID	Names	Canonical?
Q6P387-1	1	yes
Q6P387-2	2

RefSeq proteins (2): NP_001094343, NP_689550* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027836	DUF4529	Family

Pfam: PF15032

UniProt features (10 total): sequence variant 5, chain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P387-F1	50.10	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, MGGAAGTG_GABP_B, GEORGES_TARGETS_OF_MIR192_AND_MIR215, THUM_SYSTOLIC_HEART_FAILURE_DN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, chr16q23, ARID5B_TARGET_GENES, ATF6_TARGET_GENES, FEV_TARGET_GENES, FOXN3_TARGET_GENES, HOXB6_TARGET_GENES, ZNF257_TARGET_GENES, ZNF597_TARGET_GENES, MIR548AJ_3P_MIR548X_3P, MIR3529_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleoplasm (GO:0005654), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C16orf46	GCSH	P23434	539
C16orf46	IFT56	A0AVF1	478
C16orf46	CCDC183	Q5T5S1	448
C16orf46	IGKV2-28	A0A075B6P5	431
C16orf46	PRR14L	Q5THK1	403
C16orf46	ANKDD1A	Q495B1	397
C16orf46	CPSF2	Q9P2I0	371
C16orf46	PLEKHO2	Q8TD55	368
C16orf46	TAF3	Q5VWG9	366
C16orf46	CCDC91	Q7Z6B0	351
C16orf46	MVB12B	Q9H7P6	348
C16orf46	CSN1S1	P47710	324
C16orf46	RABL6	Q3YEC7	304
C16orf46	INS-IGF2	F8WCM5	300
C16orf46	RUSF1	Q96GQ5	297

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ANKRA2	C16orf46	psi-mi:“MI:0407”(direct interaction)	0.440
C16orf46	SNRPB	psi-mi:“MI:0915”(physical association)	0.400
C16orf46	FAT3	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (6): FAT3 (Affinity Capture-MS), C16orf46 (Proximity Label-MS), FAT3 (Affinity Capture-MS), C16orf46 (Affinity Capture-RNA), C16orf46 (Cross-Linking-MS (XL-MS)), RPL12 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2A8T7, A6NCN8, A6NFR6, A6NHR8, B2RW88, O12165, P03331, P18801, P22378, Q0P670, Q0VD86, Q0VF49, Q1LZE2, Q1RMX6, Q32KP7, Q3B8N5, Q3KPS4, Q3SZT6, Q3SZW6, Q3TTI8, Q3ULG3, Q5JTZ5, Q5PR19, Q5R498, Q67926, Q68FQ8, Q6P387, Q6PEX7, Q6ZV65, Q73370, Q75009, Q80VY2, Q86WR6, Q8BII1, Q8C5S3, Q8IYM0, Q8N4L4, Q8N6T0, Q8TAL5, Q8WUB2

Diamond homologs: Q4R912, Q6AXX2, Q6P387, Q8BHB7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

774 predictions. Top by Δscore:

Variant	Effect	Δscore
16:81063744:A:AC	donor_gain	1.0000
16:81063744:ACTG:A	donor_gain	1.0000
16:81063745:C:CC	donor_gain	1.0000
16:81063745:CTGC:C	donor_gain	1.0000
16:81062749:C:CT	acceptor_gain	0.9900
16:81063737:GATAC:G	donor_loss	0.9900
16:81063738:ATAC:A	donor_loss	0.9900
16:81063739:TAC:T	donor_loss	0.9900
16:81063740:ACTCA:A	donor_loss	0.9900
16:81063741:C:CG	donor_loss	0.9900
16:81063742:T:TC	donor_loss	0.9900
16:81063743:CA:C	donor_loss	0.9900
16:81063744:ACTGC:A	donor_gain	0.9900
16:81063745:CTG:C	donor_gain	0.9900
16:81063745:CTGCC:C	donor_gain	0.9900
16:81063821:G:T	acceptor_gain	0.9900
16:81066192:CCAGA:C	donor_gain	0.9900
16:81066843:C:CT	acceptor_gain	0.9900
16:81066849:A:T	acceptor_gain	0.9900
16:81077131:CCTA:C	donor_loss	0.9900
16:81077132:CTA:C	donor_loss	0.9900
16:81077133:TA:T	donor_loss	0.9900
16:81077134:ACCTG:A	donor_loss	0.9900
16:81062139:CTG:C	acceptor_loss	0.9800
16:81062140:T:G	acceptor_loss	0.9800
16:81062767:A:T	acceptor_gain	0.9800
16:81063820:C:CT	acceptor_gain	0.9800
16:81063994:C:CC	acceptor_gain	0.9800
16:81077014:AGTG:A	donor_gain	0.9800
16:81077033:C:CA	donor_gain	0.9800

AlphaMissense

2585 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:81063755:C:A	W67C	0.992
16:81063755:C:G	W67C	0.992
16:81063757:A:G	W67R	0.989
16:81063757:A:T	W67R	0.989
16:81062129:A:G	W74R	0.983
16:81062129:A:T	W74R	0.983
16:81062127:C:A	W74C	0.981
16:81062127:C:G	W74C	0.981
16:81061845:A:C	F168L	0.974
16:81061845:A:T	F168L	0.974
16:81061847:A:G	F168L	0.974
16:81063748:C:G	A70P	0.973
16:81063812:A:C	S48R	0.973
16:81063812:A:T	S48R	0.973
16:81063814:T:G	S48R	0.973
16:81063756:C:G	W67S	0.966
16:81063825:A:G	L44P	0.946
16:81062128:C:G	W74S	0.938
16:81062137:A:T	V71D	0.934
16:81063757:A:C	W67G	0.923
16:81062036:A:G	C105R	0.921
16:81062132:C:G	G73R	0.919
16:81062132:C:T	G73R	0.919
16:81061200:G:C	S383R	0.916
16:81061200:G:T	S383R	0.916
16:81061202:T:G	S383R	0.916
16:81062132:C:A	G73W	0.915
16:81063747:G:T	A70E	0.912
16:81062107:G:T	A81D	0.911
16:81062105:A:G	C82R	0.909

dbSNP variants (sampled 300 via entrez): RS1000002000 (16:81055090 A>G), RS1000038060 (16:81055419 C>T), RS1000116315 (16:81079080 C>T), RS1000192021 (16:81071830 A>T), RS1000215805 (16:81076772 T>C), RS1000365602 (16:81074662 C>G), RS1000398485 (16:81076736 T>C), RS1000479021 (16:81072779 G>C), RS1000496855 (16:81056925 G>A), RS1000567140 (16:81061493 C>A), RS1000636466 (16:81068482 C>A,T), RS1000685623 (16:81077269 A>G,T), RS1000771180 (16:81076549 T>C), RS1000773724 (16:81057325 C>G), RS1000839960 (16:81064176 G>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
GCST000253_10	Attention deficit hyperactivity disorder and conduct disorder	7.000000e-06
GCST005958_20	Waist-to-hip ratio adjusted for BMI (age >50)	4.000000e-06
GCST005962_30	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-06
GCST007638_48	Glycine levels	1.000000e-41

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0009767	glycine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	increases expression	1
cordycepin	decreases expression	1
Am 580	decreases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Rosiglitazone	decreases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	increases expression	1
Catechin	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Sodium Dodecyl Sulfate	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Valproic Acid	decreases expression	1

Clinical trials (associated diseases)

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