C19orf25

Summary

C19orf25 (chromosome 19 open reading frame 25, HGNC:26711) is a protein-coding gene on chromosome 19p13.3, encoding UPF0449 protein C19orf25 (Q9UFG5). It is a selective cancer dependency (DepMap: 22.3% of cell lines).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 9 total
• Cancer dependency (DepMap): dependent in 22.3% of screened cell lines
• MANE Select transcript: NM_152482

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26711
Approved symbol	C19orf25
Name	chromosome 19 open reading frame 25
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36666
Ensembl gene	ENSG00000119559
Ensembl biotype	protein_coding
Entrez	148223

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 19 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000427685, ENST00000436106, ENST00000585675, ENST00000586564, ENST00000588427, ENST00000588849, ENST00000588871, ENST00000589421, ENST00000590621, ENST00000591027, ENST00000592486, ENST00000592605, ENST00000592872, ENST00000651077, ENST00000908722, ENST00000908723, ENST00000914525, ENST00000914526, ENST00000914527, ENST00000914528, ENST00000914529, ENST00000962107

RefSeq mRNA: 1 — MANE Select: NM_152482 NM_152482

CCDS: CCDS45898

Canonical transcript exons

ENST00000585675 — 3 exons

Exon	Start	End
ENSE00003522551	1478774	1478905
ENSE00003899389	1479163	1479215
ENSE00003903626	1473201	1475258

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 91.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.9879 / max 104.2428, expressed in 1817 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178020	16.3592	1817
178021	0.6287	252

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	91.56	gold quality
anterior cingulate cortex	UBERON:0009835	91.41	gold quality
right frontal lobe	UBERON:0002810	90.98	gold quality
amygdala	UBERON:0001876	90.79	gold quality
granulocyte	CL:0000094	90.58	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.40	gold quality
spinal cord	UBERON:0002240	90.35	gold quality
hypothalamus	UBERON:0001898	90.25	gold quality
mucosa of transverse colon	UBERON:0004991	89.71	gold quality
prefrontal cortex	UBERON:0000451	89.34	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.32	gold quality
putamen	UBERON:0001874	89.22	gold quality
adenohypophysis	UBERON:0002196	89.10	gold quality
nucleus accumbens	UBERON:0001882	88.91	gold quality
apex of heart	UBERON:0002098	88.85	gold quality
substantia nigra	UBERON:0002038	88.83	gold quality
lower esophagus mucosa	UBERON:0035834	88.81	gold quality
cerebellar hemisphere	UBERON:0002245	88.80	gold quality
caudate nucleus	UBERON:0001873	88.64	gold quality
cerebellar cortex	UBERON:0002129	88.63	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.59	gold quality
metanephros cortex	UBERON:0010533	88.56	gold quality
pituitary gland	UBERON:0000007	88.03	gold quality
cerebellum	UBERON:0002037	87.68	gold quality
neocortex	UBERON:0001950	87.65	gold quality
midbrain	UBERON:0001891	87.56	gold quality
frontal cortex	UBERON:0001870	87.31	gold quality
right lobe of thyroid gland	UBERON:0001119	87.19	gold quality
forebrain	UBERON:0001890	86.91	gold quality
left lobe of thyroid gland	UBERON:0001120	86.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting C19orf25, 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-6798-5P	100.00	65.77	699
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-128-1-5P	99.33	60.46	332
HSA-MIR-128-2-5P	99.33	60.83	311
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-7109-5P	99.18	66.13	1057
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-7851-3P	98.72	64.88	980
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-6765-3P	97.83	64.59	1165
HSA-MIR-4640-5P	97.42	66.33	1543

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 22.3% of screened cell lines.

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch73-238c9.1	ENSDARG00000103619
mus_musculus	2310011J03Rik	ENSMUSG00000020133
rattus_norvegicus	C7h19orf25	ENSRNOG00000079774

Protein

Protein identifiers

UPF0449 protein C19orf25 — Q9UFG5 (reviewed: Q9UFG5)

All UniProt accessions (7): Q9UFG5, A0A087WUU5, E7EP72, K7EK56, K7ELZ1, K7EQW1, K7ER12

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the UPF0449 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UFG5-1	1	yes
Q9UFG5-2	2

RefSeq proteins (1): NP_689695* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028227	UPF0449	Family

Pfam: PF15136

UniProt features (4 total): chain 1, coiled-coil region 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UFG5-F1	83.75	0.54

Functional residue map

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

Post-translational modifications (1): 63

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 60 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CUI_TCF21_TARGETS_2_UP, chr19p13, KOYAMA_SEMA3B_TARGETS_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, ATF6_TARGET_GENES, ELF2_TARGET_GENES, HMG20B_TARGET_GENES, KMT2D_TARGET_GENES, LMTK3_TARGET_GENES, NAB2_TARGET_GENES, SKIL_TARGET_GENES, ZFHX3_TARGET_GENES, ZFP3_TARGET_GENES, ZFP91_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

332 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C19orf25	CBR4	Q8N4T8	556
C19orf25	ZNF623	O75123	520
C19orf25	RINT1	Q6NUQ1	507
C19orf25	TEDC1	Q86SX3	479
C19orf25	FAM174C	Q9BVV8	477
C19orf25	TEDC2	Q7L2K0	446
C19orf25	ZWILCH	Q9H900	420
C19orf25	ZWINT	O95229	419
C19orf25	PCMT1	P22061	418
C19orf25	SEPTIN8	Q92599	403
C19orf25	REXO1	Q8N1G1	396
C19orf25	CBARP	Q8N350	395
C19orf25	ZW10	O43264	371
C19orf25	ATP8B3	O60423	371
C19orf25	PRPF38B	Q5VTL8	368

IntAct

133 interactions, top by confidence:

A	B	Type	Score
RINT1	NBAS	psi-mi:“MI:0914”(association)	0.830
STX18	NBAS	psi-mi:“MI:0914”(association)	0.810
RINT1	C19orf25	psi-mi:“MI:0915”(physical association)	0.800
BNIP1	NBAS	psi-mi:“MI:0914”(association)	0.640
FPR2	ARL6IP5	psi-mi:“MI:0914”(association)	0.640
ZW10	KNTC1	psi-mi:“MI:0914”(association)	0.600
INSR	PIK3R2	psi-mi:“MI:2364”(proximity)	0.570
C19orf25	EPS8	psi-mi:“MI:0915”(physical association)	0.560
SAT1	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
BAIAP2	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
EPS8	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
C19orf25	SAT1	psi-mi:“MI:0915”(physical association)	0.560
C19orf25	BAIAP2	psi-mi:“MI:0915”(physical association)	0.560
Zw10	NBAS	psi-mi:“MI:0914”(association)	0.560
C19orf25	MEI4	psi-mi:“MI:0915”(physical association)	0.560
BORCS6	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
CRX	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
INSYN1	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
C19orf25	PNMA3	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
KRT75	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
KRTAP1-3	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
NECAB2	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
ARFIP2	C19orf25	psi-mi:“MI:0915”(physical association)	0.560
DRC12	C19orf25	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (126): C19orf25 (Two-hybrid), C19orf25 (Two-hybrid), C19orf25 (Two-hybrid), C19orf25 (Affinity Capture-MS), C19orf25 (Affinity Capture-MS), C19orf25 (Affinity Capture-MS), C19orf25 (Affinity Capture-MS), C19orf25 (Affinity Capture-MS), C19orf25 (Affinity Capture-MS), C19orf25 (Two-hybrid), C19orf25 (Affinity Capture-MS), C19orf25 (Two-hybrid), C19orf25 (Affinity Capture-Western), C19orf25 (Affinity Capture-MS), C19orf25 (Proximity Label-MS)

ESM2 similar proteins: A0JNH6, A0JNT9, A1A5D9, A5PJP1, A6NGB0, A7YWC8, B7ZNG0, O15049, O75154, O95996, P0C7N4, P58660, Q1LZF3, Q29RS0, Q2M1P5, Q2NL98, Q2TAC2, Q3LUD3, Q3TMW1, Q3UMT1, Q3V0F0, Q494R4, Q4QRL3, Q5ND29, Q5TZA2, Q6NSJ2, Q6NZW0, Q6PHN1, Q6QZQ4, Q6ZP65, Q7JVA5, Q8BP01, Q8C7U1, Q8CHW5, Q8CJ40, Q8N283, Q8N6Y0, Q8NFZ5, Q8TF21, Q91VJ2

Diamond homologs: Q1LZF3, Q28C26, Q6AY72, Q9D7E4, Q9UFG5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 106 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
COPI-dependent Golgi-to-ER retrograde traffic	8	14.1×	3e-05
Golgi-to-ER retrograde transport	5	10.5×	7e-03
Intra-Golgi and retrograde Golgi-to-ER traffic	6	10.0×	4e-03
G alpha (q) signalling events	7	6.4×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	7	25.9×	6e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

873 predictions. Top by Δscore:

Variant	Effect	Δscore
19:1461956:C:A	acceptor_gain	1.0000
19:1461957:GTCCA:G	acceptor_loss	1.0000
19:1461958:TCCAG:T	acceptor_loss	1.0000
19:1461959:CCAG:C	acceptor_loss	1.0000
19:1461961:A:AG	acceptor_gain	1.0000
19:1461961:AG:A	acceptor_gain	1.0000
19:1461961:AGG:A	acceptor_loss	1.0000
19:1461962:G:GG	acceptor_gain	1.0000
19:1461962:GG:G	acceptor_gain	1.0000
19:1461962:GGA:G	acceptor_gain	1.0000
19:1461962:GGAGT:G	acceptor_gain	1.0000
19:1462165:G:GG	donor_gain	1.0000
19:1462170:GAC:G	donor_gain	1.0000
19:1462173:TACAG:T	donor_loss	1.0000
19:1462175:CAG:C	donor_loss	1.0000
19:1462178:GTCGG:G	donor_loss	1.0000
19:1462179:T:A	donor_loss	1.0000
19:1465153:AG:A	acceptor_gain	1.0000
19:1465153:AGGC:A	acceptor_loss	1.0000
19:1465154:GG:G	acceptor_gain	1.0000
19:1465154:GGC:G	acceptor_gain	1.0000
19:1465154:GGCA:G	acceptor_gain	1.0000
19:1478776:T:A	donor_gain	1.0000
19:1461949:C:A	acceptor_gain	0.9900
19:1461959:CCAGG:C	acceptor_gain	0.9900
19:1461960:CAGG:C	acceptor_gain	0.9900
19:1461961:AGGA:A	acceptor_gain	0.9900
19:1461962:GGAG:G	acceptor_gain	0.9900
19:1465153:A:AG	acceptor_gain	0.9900
19:1465154:G:GG	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000338202 (19:1474357 A>G), RS1000757303 (19:1480835 C>A,G,T), RS1000945533 (19:1473629 G>A), RS1001080316 (19:1477832 C>A), RS1001231958 (19:1480913 C>T), RS1001359445 (19:1479137 C>G), RS1001379153 (19:1474681 C>T), RS1001460377 (19:1474855 A>C,G), RS1001581951 (19:1476682 G>A), RS1001932998 (19:1477925 C>T), RS1002445436 (19:1473863 T>C), RS1002496389 (19:1480189 C>T), RS1002549337 (19:1472853 G>A), RS1002753262 (19:1479141 C>A,G), RS1002834331 (19:1479998 G>A,T)

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

2 associations (top):

Study	Trait	p-value
GCST008153_26	Lean body mass	5.000000e-06
GCST008161_38	Waist circumference adjusted for body mass index	3.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004995	lean body mass
EFO:0007789	BMI-adjusted waist circumference

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
Valproic Acid	increases methylation, affects expression, increases expression	4
bisphenol A	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
jinfukang	increases expression	1
Sunitinib	decreases expression	1
Arsenic	affects methylation	1
Cisplatin	increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Antirheumatic Agents	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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