C16orf78

Summary

C16orf78 (chromosome 16 open reading frame 78, HGNC:28479) is a protein-coding gene on chromosome 16q12.1, encoding Uncharacterized protein C16orf78 (Q8WTQ4).

Located in nucleus.

Source: NCBI Gene 123970 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_144602

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28479
Approved symbol	C16orf78
Name	chromosome 16 open reading frame 78
Location	16q12.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC33367
Ensembl gene	ENSG00000166152
Ensembl biotype	protein_coding
Entrez	123970

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000299191

RefSeq mRNA: 1 — MANE Select: NM_144602 NM_144602

CCDS: CCDS10738

Canonical transcript exons

ENST00000299191 — 5 exons

Exon	Start	End
ENSE00001100277	49377731	49377850
ENSE00001100290	49378470	49378593
ENSE00001100292	49396423	49396678
ENSE00001164994	49373804	49374089
ENSE00001301834	49399131	49399431

Expression profiles

Bgee: expression breadth broad, 22 present calls, max score 94.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0435 / max 34.2825, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
153971	0.0291	3
153973	0.0103	4
153972	0.0041	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.25	gold quality
right testis	UBERON:0004534	88.71	gold quality
left testis	UBERON:0004533	88.36	gold quality
testis	UBERON:0000473	85.76	gold quality
adult organism	UBERON:0007023	73.19	gold quality
cardiac muscle of right atrium	UBERON:0003379	71.95	gold quality
pancreatic ductal cell	CL:0002079	71.78	silver quality
tibialis anterior	UBERON:0001385	71.77	silver quality
left ventricle myocardium	UBERON:0006566	71.59	gold quality
kidney epithelium	UBERON:0004819	70.51	gold quality
upper arm skin	UBERON:0004263	68.94	gold quality
deltoid	UBERON:0001476	62.46	gold quality
nasal cavity epithelium	UBERON:0005384	60.18	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	60.15	gold quality
myocardium	UBERON:0002349	59.60	gold quality
lower lobe of lung	UBERON:0008949	58.82	silver quality
vena cava	UBERON:0004087	58.79	silver quality
layer of synovial tissue	UBERON:0007616	58.32	gold quality
ileal mucosa	UBERON:0000331	56.34	silver quality
substantia nigra pars compacta	UBERON:0001965	55.55	gold quality
cardia of stomach	UBERON:0001162	55.25	gold quality
epithelium of mammary gland	UBERON:0003244	55.12	gold quality
lateral globus pallidus	UBERON:0002476	55.04	gold quality
mammary duct	UBERON:0001765	54.95	gold quality
ventral tegmental area	UBERON:0002691	54.90	gold quality
saphenous vein	UBERON:0007318	54.77	gold quality
pericardium	UBERON:0002407	54.70	gold quality
urethra	UBERON:0000057	54.61	gold quality
superficial temporal artery	UBERON:0001614	54.59	gold quality
pharyngeal mucosa	UBERON:0000355	54.57	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

2 targeting C16orf78, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	4933402J07Rik	ENSMUSG00000069971
rattus_norvegicus	C19h16orf78	ENSRNOG00000024182

Protein

Protein identifiers

Uncharacterized protein C16orf78 — Q8WTQ4 (reviewed: Q8WTQ4)

All UniProt accessions (1): Q8WTQ4

RefSeq proteins (1): NP_653203* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029171	DUF4638	Family

Pfam: PF15472

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WTQ4-F1	55.37	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): YGACNNYACAR_UNKNOWN, ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, GSE13306_LAMINA_PROPRIA_VS_SPLEEN_TREG_DN, GSE15324_ELF4_KO_VS_WT_NAIVE_CD8_TCELL_DN, GSE27786_CD8_TCELL_VS_MONO_MAC_DN, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_UP, GSE7460_CTRL_VS_FOXP3_OVEREXPR_TCONV_UP, GSE7460_CTRL_VS_FOXP3_OVEREXPR_TCONV_1_UP, GSE3691_CONVENTIONAL_VS_PLASMACYTOID_DC_SPLEEN_DN, GSE19888_NO_PRETREAT_VS_ADENOSINE_A3R_INHIBITOR_PRETREATED_MAST_CELL_TCELL_MEMBRANES_ACT_UP, GSE22589_SIV_VS_HIV_AND_SIV_INFECTED_DC_UP, GSE22589_HEALTHY_VS_HIV_INFECTED_DC_DN, chr16q12

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

178 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C16orf78	CNEP1R1	Q8N9A8	596
C16orf78	HEATR3	Q7Z4Q2	482
C16orf78	TENT4B	Q8NDF8	447
C16orf78	SNX20	Q7Z614	418
C16orf78	CCDC142	Q17RM4	399
C16orf78	GOLGA8H	P0CJ92	395
C16orf78	GOLGA8R	I6L899	391
C16orf78	ZNF423	Q2M1K9	350
C16orf78	C2orf81	A6NN90	339
C16orf78	BRICD5	Q6PL45	323
C16orf78	SHCBP1	Q8NEM2	321
C16orf78	GOLGA8Q	H3BV12	300
C16orf78	AKTIP	Q9H8T0	300
C16orf78	WDR54	Q9H977	295
C16orf78	GOLGA8N	F8WBI6	290
C16orf78	RNF151	Q2KHN1	290

IntAct

4 interactions, top by confidence:

A	B	Type	Score
C16orf78	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
C16orf78	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
KIN	C16orf78	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (4): C16orf78 (Reconstituted Complex), C16orf78 (Proximity Label-MS), C16orf78 (Biochemical Activity), C16orf78 (Biochemical Activity)

ESM2 similar proteins: A0A1B0GVB3, A0A1B0GVH6, A2RRY8, A4IGV6, A6NHR8, B3DHS1, E1B9I5, O74317, O95561, P03319, P03320, P0C9Z5, P0C9Z6, P10260, P36353, P40744, P40745, Q06616, Q09280, Q09424, Q2KIL1, Q2KIR0, Q32KT7, Q32LB6, Q3T028, Q3TTI8, Q496A3, Q5NC83, Q5SQS8, Q5XIU7, Q68FQ8, Q6DFB0, Q6ZNM6, Q6ZV65, Q811V6, Q8IWA6, Q8N9R6, Q8R0E5, Q8TAL5, Q8WTQ4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

7 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

551 predictions. Top by Δscore:

Variant	Effect	Δscore
16:49377726:TTCAG:T	acceptor_loss	1.0000
16:49377727:TCAG:T	acceptor_loss	1.0000
16:49377729:A:AG	acceptor_gain	1.0000
16:49377729:AG:A	acceptor_loss	1.0000
16:49377730:G:GA	acceptor_gain	1.0000
16:49377730:GA:G	acceptor_gain	1.0000
16:49377847:GCAG:G	donor_gain	1.0000
16:49377848:CAGGT:C	donor_loss	1.0000
16:49377849:AGGTA:A	donor_loss	1.0000
16:49377851:GTAAT:G	donor_loss	1.0000
16:49378467:AAG:A	acceptor_gain	1.0000
16:49378468:A:G	acceptor_gain	1.0000
16:49396646:G:GT	donor_gain	1.0000
16:49396662:G:GT	donor_gain	1.0000
16:49396675:GCCG:G	donor_gain	1.0000
16:49396677:CGGT:C	donor_loss	1.0000
16:49396678:GGTG:G	donor_loss	1.0000
16:49396679:G:GG	donor_gain	1.0000
16:49396679:G:T	donor_loss	1.0000
16:49396680:T:A	donor_loss	1.0000
16:49399128:CA:C	acceptor_loss	1.0000
16:49399129:A:AG	acceptor_gain	1.0000
16:49399130:G:GG	acceptor_gain	1.0000
16:49399130:GA:G	acceptor_gain	1.0000
16:49399130:GATAC:G	acceptor_gain	1.0000
16:49374088:AG:A	donor_loss	0.9900
16:49374090:G:C	donor_loss	0.9900
16:49374091:T:A	donor_loss	0.9900
16:49374941:A:AG	donor_gain	0.9900
16:49377730:GAA:G	acceptor_gain	0.9900

AlphaMissense

1776 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:49399249:T:C	F257L	0.946
16:49399251:C:A	F257L	0.946
16:49399251:C:G	F257L	0.946
16:49399142:T:C	L221S	0.926
16:49399186:G:C	A236P	0.925
16:49399166:T:C	L229S	0.884
16:49399177:T:C	C233R	0.880
16:49399179:C:G	C233W	0.870
16:49399178:G:A	C233Y	0.865
16:49399145:C:T	S222F	0.863
16:49399177:T:A	C233S	0.848
16:49399178:G:C	C233S	0.848
16:49399209:C:A	H243Q	0.842
16:49399209:C:G	H243Q	0.842
16:49399155:C:A	N225K	0.840
16:49399155:C:G	N225K	0.840
16:49399140:G:C	R220S	0.831
16:49399140:G:T	R220S	0.831
16:49396669:T:C	L214P	0.830
16:49396669:T:A	L214Q	0.829
16:49399250:T:C	F257S	0.829
16:49399175:T:C	L232S	0.824
16:49399136:T:C	L219P	0.821
16:49399190:G:T	G237V	0.820
16:49399169:T:C	L230P	0.815
16:49399250:T:G	F257C	0.807
16:49374050:G:C	W37C	0.804
16:49374050:G:T	W37C	0.804
16:49399193:T:C	M238T	0.800
16:49396674:T:C	C216R	0.795

dbSNP variants (sampled 300 via entrez): RS1000052412 (16:49378961 G>A), RS1000221764 (16:49391482 T>A), RS1000303338 (16:49397206 C>T), RS1000403878 (16:49378746 C>A), RS1000409744 (16:49396816 G>A), RS1000587474 (16:49392730 C>A,T), RS1000637282 (16:49396235 C>A), RS1000689349 (16:49398550 T>A,C), RS1000752273 (16:49390289 T>C), RS1000762322 (16:49398277 G>T), RS1000838080 (16:49376248 AT>A), RS1001000906 (16:49381288 T>G), RS1001001851 (16:49387302 TGTC>T), RS1001054177 (16:49386959 C>T), RS1001091533 (16:49389923 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
GCST004640_16	Western dietary pattern	5.000000e-06
GCST007576_281	Chronotype	1.000000e-09
GCST007576_401	Chronotype	1.000000e-09
GCST008551_8	Simvastatin-induced myopathy	7.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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