C1orf159

Summary

C1orf159 (chromosome 1 open reading frame 159, HGNC:26062) is a protein-coding gene on chromosome 1p36.33, encoding Uncharacterized protein C1orf159 (Q96HA4).

Predicted to be located in membrane.

Source: NCBI Gene 54991 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 22 total — 1 pathogenic
• MANE Select transcript: NM_017891

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26062
Approved symbol	C1orf159
Name	chromosome 1 open reading frame 159
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20584
Ensembl gene	ENSG00000131591
Ensembl biotype	protein_coding
Entrez	54991

Gene structure

Transcript identifiers

Ensembl transcripts: 54 — 45 protein_coding, 4 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000379319, ENST00000379320, ENST00000379325, ENST00000379339, ENST00000421241, ENST00000427787, ENST00000434641, ENST00000442117, ENST00000462097, ENST00000464905, ENST00000465822, ENST00000467751, ENST00000472741, ENST00000473600, ENST00000475119, ENST00000477196, ENST00000480643, ENST00000482816, ENST00000487177, ENST00000871969, ENST00000871970, ENST00000871971, ENST00000871972, ENST00000871973, ENST00000871974, ENST00000871975, ENST00000871976, ENST00000871977, ENST00000871978, ENST00000871979, ENST00000871980, ENST00000871981, ENST00000871982, ENST00000871983, ENST00000871984, ENST00000934528, ENST00000934529, ENST00000934530, ENST00000934531, ENST00000934532, ENST00000934533, ENST00000934534, ENST00000934535, ENST00000934536, ENST00000962840, ENST00000962841, ENST00000962842, ENST00000962843, ENST00000962844, ENST00000962845, ENST00000962846, ENST00000962847, ENST00000962848, ENST00000962849

RefSeq mRNA: 3 — MANE Select: NM_017891 NM_001330306, NM_001363525, NM_017891

CCDS: CCDS7, CCDS81250, CCDS85917

Canonical transcript exons

ENST00000421241 — 10 exons

Exon	Start	End
ENSE00001902417	1116060	1116089
ENSE00002711450	1091991	1092103
ENSE00003463192	1087502	1087597
ENSE00003506442	1084353	1084383
ENSE00003592709	1090353	1090428
ENSE00003614342	1084481	1084506
ENSE00003615395	1081823	1082987
ENSE00003652001	1091472	1091565
ENSE00003678908	1085878	1086012
ENSE00003789790	1087139	1087204

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 91.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.8699 / max 88.5238, expressed in 1633 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9698	4.8252	1630
9695	0.0392	12
9699	0.0056	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.39	gold quality
right testis	UBERON:0004534	91.25	gold quality
lower esophagus mucosa	UBERON:0035834	89.09	gold quality
testis	UBERON:0000473	87.56	gold quality
right uterine tube	UBERON:0001302	87.42	gold quality
right frontal lobe	UBERON:0002810	86.63	gold quality
mucosa of transverse colon	UBERON:0004991	86.34	gold quality
granulocyte	CL:0000094	85.97	gold quality
metanephros cortex	UBERON:0010533	85.37	gold quality
anterior cingulate cortex	UBERON:0009835	84.83	gold quality
cingulate cortex	UBERON:0003027	84.68	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.91	gold quality
transverse colon	UBERON:0001157	83.85	gold quality
apex of heart	UBERON:0002098	83.68	gold quality
body of stomach	UBERON:0001161	83.32	gold quality
esophagus mucosa	UBERON:0002469	83.29	gold quality
skin of abdomen	UBERON:0001416	83.24	gold quality
cerebellar hemisphere	UBERON:0002245	82.85	gold quality
skin of leg	UBERON:0001511	82.81	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.75	gold quality
cerebellar cortex	UBERON:0002129	82.71	gold quality
nucleus accumbens	UBERON:0001882	82.69	gold quality
ectocervix	UBERON:0012249	82.25	gold quality
amygdala	UBERON:0001876	82.01	gold quality
caudate nucleus	UBERON:0001873	81.79	gold quality
endocervix	UBERON:0000458	81.76	gold quality
esophagus	UBERON:0001043	81.72	gold quality
putamen	UBERON:0001874	81.71	gold quality
minor salivary gland	UBERON:0001830	81.69	gold quality
mucosa of stomach	UBERON:0001199	81.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting C1orf159, 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-4447	99.85	67.81	2900
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-3928-5P	98.50	67.48	980
HSA-MIR-6806-3P	98.50	67.31	980
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-3189-5P	97.55	66.71	655
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-4296	96.35	63.55	1233
HSA-MIR-6796-5P	95.37	66.08	1120
HSA-MIR-2861	95.24	65.47	1056
HSA-MIR-4258	90.68	62.19	164

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-157b11.12	ENSDARG00000086336
mus_musculus	9430015G10Rik	ENSMUSG00000059939
rattus_norvegicus	C5h1orf159	ENSRNOG00000020199

Protein

Protein identifiers

Uncharacterized protein C1orf159 — Q96HA4 (reviewed: Q96HA4)

All UniProt accessions (10): B2REC4, B2REC5, Q96HA4, J3KSJ6, J3KT48, J3QKM1, J3QRL0, J3QSF0, Q5T2W7, Q5T2W9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (5)

UniProt ID	Names	Canonical?
Q96HA4-1	1	yes
Q96HA4-2	2
Q96HA4-3	3
Q96HA4-4	4
Q96HA4-5	5

RefSeq proteins (3): NP_001317235, NP_001350454, NP_060361* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027888	DUF4501	Family

Pfam: PF14946

UniProt features (17 total): splice variant 7, glycosylation site 3, region of interest 2, compositionally biased region 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HA4-F1	49.03	0.03

Functional residue map

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

Glycosylation sites (3): 104, 111, 128

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): MODULE_97, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP, MODULE_182, AIYAR_COBRA1_TARGETS_UP, MARSON_BOUND_BY_E2F4_UNSTIMULATED, JIANG_VHL_TARGETS, chr1p36, HUTTMANN_B_CLL_POOR_SURVIVAL_UP, MODULE_358, BHAT_ESR1_TARGETS_VIA_AKT1_UP, MODULE_525, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP, MYC_UP.V1_DN, SRC_UP.V1_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf159	DNHD1	Q96M86	533
C1orf159	PTCD2	Q8WV60	527
C1orf159	ZNHIT2	Q9UHR6	509
C1orf159	ZNF106	Q9H2Y7	507
C1orf159	FRMD8	Q9BZ67	506
C1orf159	BOD1L1	Q8NFC6	498
C1orf159	FRRS1L	Q9P0K9	494
C1orf159	SSH2	Q76I76	471
C1orf159	COG1	Q8WTW3	470
C1orf159	DHX29	Q7Z478	464
C1orf159	PROM2	Q8N271	459
C1orf159	SCAF11	Q99590	456
C1orf159	SIX5	Q8N196	455
C1orf159	OTUD5	Q96G74	448
C1orf159	FAM149B1	Q96BN6	426

IntAct

8 interactions, top by confidence:

A	B	Type	Score
GBP5	GBP1	psi-mi:“MI:0914”(association)	0.720
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
	TMEM223	psi-mi:“MI:0914”(association)	0.350
LRRC55	TMEM120B	psi-mi:“MI:0914”(association)	0.350
LGALS8	SLC22A23	psi-mi:“MI:0914”(association)	0.350
MAGEA8	METTL15	psi-mi:“MI:0914”(association)	0.350

BioGRID (19): C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-RNA), C1orf159 (Two-hybrid), TOMM6 (Two-hybrid), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-RNA), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS), C1orf159 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A4IHR5, A7UKY7, A8IHN8, D3YYI7, G3V9M2, O43559, P39881, P49796, Q13387, Q14DQ1, Q2TAM9, Q32KV8, Q3UPL5, Q4VA45, Q5VUJ9, Q5VV17, Q5XKK7, Q62392, Q673H1, Q6NV74, Q6PJ61, Q6QHK4, Q6UXB0, Q7Z6J2, Q80TE3, Q86SH2, Q8BWU3, Q8CE64, Q8IWP9, Q8N554, Q8NFT6, Q8R4T5, Q8TC41, Q8VCC6, Q8WV24, Q96HA4, Q96IQ9, Q96SQ7, Q96T92

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
980940	GRCh37/hg19 1p36.33-36.31(chr1:1-5592835)x1	Pathogenic

SpliceAI

2993 predictions. Top by Δscore:

Variant	Effect	Δscore
1:1082988:C:CC	acceptor_gain	1.0000
1:1084479:A:AC	donor_gain	1.0000
1:1084480:C:CC	donor_gain	1.0000
1:1084507:C:CC	acceptor_gain	1.0000
1:1087500:A:AC	donor_gain	1.0000
1:1087501:C:CC	donor_gain	1.0000
1:1087501:CAG:C	donor_gain	1.0000
1:1082983:CCGTA:C	acceptor_gain	0.9900
1:1082984:CGTA:C	acceptor_gain	0.9900
1:1082984:CGTAC:C	acceptor_gain	0.9900
1:1082986:TA:T	acceptor_gain	0.9900
1:1082987:AC:A	acceptor_loss	0.9900
1:1082988:C:T	acceptor_loss	0.9900
1:1082989:T:A	acceptor_loss	0.9900
1:1084385:T:C	acceptor_gain	0.9900
1:1084385:T:TC	acceptor_gain	0.9900
1:1084475:ACTT:A	donor_loss	0.9900
1:1084476:CTT:C	donor_loss	0.9900
1:1084477:TTA:T	donor_loss	0.9900
1:1084478:T:TG	donor_loss	0.9900
1:1084479:AC:A	donor_loss	0.9900
1:1084480:CG:C	donor_gain	0.9900
1:1084480:CGG:C	donor_gain	0.9900
1:1084502:CGGAG:C	acceptor_gain	0.9900
1:1084504:GAG:G	acceptor_gain	0.9900
1:1084505:AGC:A	acceptor_loss	0.9900
1:1084506:GCT:G	acceptor_loss	0.9900
1:1084507:C:CA	acceptor_loss	0.9900
1:1087439:C:CA	donor_gain	0.9900
1:1090348:CTTA:C	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000036673 (1:1106029 A>G), RS1000040358 (1:1103165 A>G), RS1000050523 (1:1083131 A>G), RS1000194837 (1:1085711 C>T), RS1000223283 (1:1089989 C>G,T), RS1000261266 (1:1101159 G>A), RS1000327601 (1:1096358 G>A), RS1000436209 (1:1117559 C>T), RS1000591988 (1:1100913 G>A), RS1000627698 (1:1111658 C>G), RS1000653408 (1:1097395 G>A), RS1000663117 (1:1097637 G>A), RS1000759538 (1:1082306 G>A), RS1000814305 (1:1091865 G>A), RS1000975579 (1:1088869 G>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:615593

GenCC curated gene-disease

Mondo (1): combined immunodeficiency due to OX40 deficiency (MONDO:0014268)

Orphanet (1): Combined immunodeficiency due to OX40 deficiency (Orphanet:431149)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	3
aristolochic acid I	increases expression	1
bisphenol F	increases expression, affects cotreatment	1
bisphenol A	decreases methylation	1
beta-lapachone	increases expression, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	increases expression, increases abundance	1
ICG 001	decreases expression	1
abrine	decreases expression	1
jinfukang	increases expression	1
MT19c compound	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Dexamethasone	increases expression, affects cotreatment	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1
Acrylamide	decreases expression	1
Magnetite Nanoparticles	increases expression, decreases methylation	1

Clinical trials (associated diseases)

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