C19orf47

Summary

C19orf47 (chromosome 19 open reading frame 47, HGNC:26723) is a protein-coding gene on chromosome 19q13.2, encoding Uncharacterized protein C19orf47 (Q8N9M1).

Located in nucleoplasm.

Source: NCBI Gene 126526 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001256441

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26723
Approved symbol	C19orf47
Name	chromosome 19 open reading frame 47
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36888
Ensembl gene	ENSG00000160392
Ensembl biotype	protein_coding
Entrez	126526

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000357884, ENST00000392035, ENST00000577617, ENST00000580606, ENST00000580977, ENST00000582006, ENST00000582734, ENST00000582783, ENST00000584868, ENST00000683109, ENST00000897518, ENST00000897519, ENST00000897520, ENST00000897521, ENST00000931071, ENST00000931072, ENST00000964670

RefSeq mRNA: 2 — MANE Select: NM_001256441 NM_001256440, NM_001256441

CCDS: CCDS58662, CCDS92619

Canonical transcript exons

ENST00000683109 — 9 exons

Exon	Start	End
ENSE00001051954	40336110	40336224
ENSE00002714499	40319536	40322376
ENSE00003488229	40324006	40324076
ENSE00003502788	40326334	40326486
ENSE00003529860	40341839	40341890
ENSE00003580264	40336320	40336407
ENSE00003589252	40333851	40333929
ENSE00003785237	40328413	40328550
ENSE00003920619	40348324	40348397

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 98.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5615 / max 100.0706, expressed in 1734 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180977	5.0990	1708
180979	0.6406	376
180975	0.4727	89
180978	0.3216	149
180980	0.0138	2
180976	0.0137	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	98.48	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.34	gold quality
gastrocnemius	UBERON:0001388	98.24	gold quality
muscle of leg	UBERON:0001383	97.02	gold quality
right atrium auricular region	UBERON:0006631	96.44	gold quality
heart left ventricle	UBERON:0002084	95.76	gold quality
cardiac atrium	UBERON:0002081	95.09	gold quality
cardiac ventricle	UBERON:0002082	94.91	gold quality
heart	UBERON:0000948	92.94	gold quality
left testis	UBERON:0004533	89.95	gold quality
right testis	UBERON:0004534	89.72	gold quality
pancreatic ductal cell	CL:0002079	87.58	silver quality
prefrontal cortex	UBERON:0000451	87.54	gold quality
testis	UBERON:0000473	87.05	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	86.81	silver quality
cortical plate	UBERON:0005343	85.51	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.95	gold quality
myocardium	UBERON:0002349	84.91	gold quality
popliteal artery	UBERON:0002250	84.33	gold quality
tibial artery	UBERON:0007610	84.31	gold quality
tendon of biceps brachii	UBERON:0008188	84.13	gold quality
aorta	UBERON:0000947	83.96	gold quality
right coronary artery	UBERON:0001625	83.83	gold quality
ascending aorta	UBERON:0001496	83.66	gold quality
thoracic aorta	UBERON:0001515	83.66	gold quality
skeletal muscle tissue	UBERON:0001134	83.64	gold quality
epithelial cell of pancreas	CL:0000083	83.61	gold quality
spinal cord	UBERON:0002240	83.60	gold quality
stromal cell of endometrium	CL:0002255	83.29	gold quality
left coronary artery	UBERON:0001626	83.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.93

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	C18H19orf47	ENSDARG00000020611
mus_musculus	2310022A10Rik	ENSMUSG00000049643
rattus_norvegicus	C1h19orf47	ENSRNOG00000018408
drosophila_melanogaster	CG16812	FBGN0032488
caenorhabditis_elegans		WBGENE00010002

Protein

Protein identifiers

Uncharacterized protein C19orf47 — Q8N9M1 (reviewed: Q8N9M1)

All UniProt accessions (8): Q8N9M1, A0A2R8Y6U9, A0A804HLH2, J3QKY6, J3QKZ5, J3QS16, J3QS80, J9JIE4

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N9M1-1	1	yes
Q8N9M1-2	2
Q8N9M1-3	3

RefSeq proteins (2): NP_001243369, NP_001243370* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013761	SAM/pointed_sf	Homologous_superfamily
IPR039161	C19orf47-like	Family
IPR040772	C19orf47_SAM	Domain
IPR041477	DUF5577	Domain

Pfam: PF17740, PF18017

UniProt features (15 total): modified residue 6, region of interest 3, splice variant 2, compositionally biased region 2, chain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9M1-F1	61.37	0.17

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 (7): 306, 351, 250, 124, 126, 151, 280

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, MYB_Q3, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, GTGACTT_MIR224, MYB_Q5_01, SCGGAAGY_ELK1_02, MYB_Q6, CHEN_METABOLIC_SYNDROM_NETWORK, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, ARID5B_TARGET_GENES, ARNT2_TARGET_GENES, CBX7_TARGET_GENES, DIDO1_TARGET_GENES, FEV_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

310 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C19orf47	ACTMAP	Q5BKX5	480
C19orf47	PRMT2IP	Q6ZRI6	447
C19orf47	ZNF780A	O75290	445
C19orf47	FAM124A	Q86V42	433
C19orf47	TIGD2	Q4W5G0	433
C19orf47	TTC9B	Q8N6N2	431
C19orf47	ZNF546	Q86UE3	419
C19orf47	ZBTB45	Q96K62	419
C19orf47	CSTPP1	Q9H6J7	419
C19orf47	ZNF780B	Q9Y6R6	417
C19orf47	TMEM91	Q6ZNR0	400
C19orf47	GPATCH1	Q9BRR8	380
C19orf47	DMAC2	Q9NW81	377
C19orf47	ACAP3	Q96P50	367
C19orf47	SERTAD3	Q9UJW9	358

IntAct

12 interactions, top by confidence:

A	B	Type	Score
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
C19orf47	NTM	psi-mi:“MI:0915”(physical association)	0.560
NTM	C19orf47	psi-mi:“MI:0915”(physical association)	0.560
YWHAQ	MCRIP1	psi-mi:“MI:0914”(association)	0.350
DDX39B	RBM33	psi-mi:“MI:0914”(association)	0.350
RTCB	MCRIP1	psi-mi:“MI:0914”(association)	0.350
SRSF1	MED19	psi-mi:“MI:2364”(proximity)	0.270
SRSF7	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
	C19orf47	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (38): C19orf47 (Two-hybrid), C19orf47 (Affinity Capture-MS), MORF4L1 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Affinity Capture-MS), C19orf47 (Proximity Label-MS), C19orf47 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8GR68, A0JPQ7, A4FV61, F7AQ22, O62666, O62674, O62676, O62678, O75151, O75152, P49140, P53349, P97432, Q13233, Q14596, Q15047, Q1LY51, Q3ZC82, Q4R6F6, Q53F19, Q5F3Z9, Q5R6F3, Q5SUE8, Q5XJV7, Q5ZJJ1, Q60698, Q60974, Q62925, Q69Z61, Q69Z99, Q6AI12, Q6NXK2, Q6PJT7, Q6ZNC4, Q7TMD5, Q80VG1, Q80XA6, Q86XL3, Q8BG81, Q8BJ05

Diamond homologs: A0JPQ7, Q8N9M1, Q8R3Y5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1327 predictions. Top by Δscore:

Variant	Effect	Δscore
19:40322372:GTGGG:G	acceptor_gain	1.0000
19:40322373:TGGG:T	acceptor_gain	1.0000
19:40322375:GG:G	acceptor_gain	1.0000
19:40322377:C:CC	acceptor_gain	1.0000
19:40324004:A:AC	donor_gain	1.0000
19:40324005:C:CC	donor_gain	1.0000
19:40324012:C:CA	donor_gain	1.0000
19:40326330:GTAC:G	donor_loss	1.0000
19:40326331:TACCT:T	donor_loss	1.0000
19:40326332:A:AC	donor_gain	1.0000
19:40326332:ACCTT:A	donor_loss	1.0000
19:40326333:C:CA	donor_loss	1.0000
19:40326333:C:CC	donor_gain	1.0000
19:40326480:AGGGC:A	acceptor_loss	1.0000
19:40326481:GGGCT:G	acceptor_loss	1.0000
19:40326482:GGC:G	acceptor_loss	1.0000
19:40326482:GGCTG:G	acceptor_gain	1.0000
19:40326483:GC:G	acceptor_loss	1.0000
19:40326484:C:CC	acceptor_gain	1.0000
19:40326484:CTG:C	acceptor_loss	1.0000
19:40326485:T:A	acceptor_loss	1.0000
19:40326485:TG:T	acceptor_gain	1.0000
19:40326486:GC:G	acceptor_loss	1.0000
19:40326487:C:CA	acceptor_loss	1.0000
19:40326487:C:CC	acceptor_gain	1.0000
19:40326488:T:A	acceptor_loss	1.0000
19:40328408:CTCA:C	donor_loss	1.0000
19:40328411:A:AC	donor_gain	1.0000
19:40328412:C:CC	donor_gain	1.0000
19:40328412:C:CG	donor_loss	1.0000

AlphaMissense

2504 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:40336129:G:T	A105D	1.000
19:40336138:A:G	L102P	1.000
19:40336141:A:T	I101N	1.000
19:40336147:A:T	I99N	1.000
19:40336156:C:T	G96D	1.000
19:40336198:A:G	L82P	1.000
19:40336222:A:G	I74T	1.000
19:40336332:A:G	F69S	1.000
19:40336341:G:T	A66D	1.000
19:40336386:A:G	F51S	1.000
19:40336394:C:A	W48C	1.000
19:40336394:C:G	W48C	1.000
19:40336396:A:G	W48R	1.000
19:40336396:A:T	W48R	1.000
19:40336130:C:G	A105P	0.999
19:40336141:A:C	I101S	0.999
19:40336145:C:G	A100P	0.999
19:40336147:A:C	I99S	0.999
19:40336153:T:A	D97V	0.999
19:40336153:T:C	D97G	0.999
19:40336153:T:G	D97A	0.999
19:40336156:C:A	G96V	0.999
19:40336157:C:G	G96R	0.999
19:40336174:A:G	L90P	0.999
19:40336198:A:T	L82H	0.999
19:40336207:A:G	L79P	0.999
19:40336222:A:C	I74S	0.999
19:40336222:A:T	I74N	0.999
19:40336320:C:A	R73M	0.999
19:40336320:C:G	R73T	0.999

dbSNP variants (sampled 300 via entrez): RS1000052697 (19:40339888 T>C), RS1000059486 (19:40300780 G>A), RS1000172926 (19:40310101 A>C), RS1000193656 (19:40323457 G>A), RS1000257910 (19:40345122 A>G), RS1000303692 (19:40307623 A>C), RS1000351266 (19:40334187 G>A,T), RS1000380264 (19:40303675 G>A), RS1000385666 (19:40306533 G>A), RS1000424866 (19:40311613 G>A), RS1000453126 (19:40338324 T>C), RS1000496320 (19:40335283 C>A), RS1000635337 (19:40332031 T>C,G), RS1000659304 (19:40343881 C>T), RS1000664668 (19:40304760 T>A)

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
GCST003818_30	Resting heart rate	1.000000e-11
GCST90002396_38	Mean reticulocyte volume	2.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Phenylmercuric Acetate	affects cotreatment, increases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
sodium arsenite	affects expression	1
coumarin	affects phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Atrazine	increases expression	1
Caffeine	decreases phosphorylation	1
Tobacco Smoke Pollution	increases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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