C1orf21

Summary

C1orf21 (chromosome 1 open reading frame 21, HGNC:15494) is a protein-coding gene on chromosome 1q25.3, encoding Uncharacterized protein C1orf21 (Q9H246).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 12 total — 1 pathogenic
• MANE Select transcript: NM_030806

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15494
Approved symbol	C1orf21
Name	chromosome 1 open reading frame 21
Location	1q25.3
Locus type	gene with protein product
Status	Approved
Aliases	PIG13
Ensembl gene	ENSG00000116667
Ensembl biotype	protein_coding
Entrez	81563

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 8 protein_coding, 4 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay

ENST00000235307, ENST00000367514, ENST00000477517, ENST00000489143, ENST00000648109, ENST00000675061, ENST00000675148, ENST00000675405, ENST00000866161, ENST00000866162, ENST00000866163, ENST00000866164, ENST00000921184, ENST00000921185, ENST00000950223

RefSeq mRNA: 1 — MANE Select: NM_030806 NM_030806

CCDS: CCDS1362

Canonical transcript exons

ENST00000235307 — 6 exons

Exon	Start	End
ENSE00000790759	184507588	184507682
ENSE00001175567	184619518	184629019
ENSE00001283926	184477386	184477603
ENSE00001444845	184387029	184387368
ENSE00003492147	184598401	184598461
ENSE00003566545	184590739	184590815

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 98.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.9818 / max 803.8024, expressed in 1696 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
7218	18.6021	1672
7220	13.1863	1558
7219	2.1855	947
7221	2.0564	835
7217	0.7802	430
7224	0.0984	37
7225	0.0728	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.07	gold quality
gastrocnemius	UBERON:0001388	97.89	gold quality
muscle of leg	UBERON:0001383	97.68	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.16	gold quality
skin of abdomen	UBERON:0001416	96.42	gold quality
ectocervix	UBERON:0012249	96.34	gold quality
rectum	UBERON:0001052	96.31	gold quality
skin of leg	UBERON:0001511	96.15	gold quality
vagina	UBERON:0000996	96.07	gold quality
tendon	UBERON:0000043	96.06	gold quality
skeletal muscle organ	UBERON:0014892	95.94	gold quality
muscle organ	UBERON:0001630	95.93	gold quality
tibia	UBERON:0000979	95.79	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	95.64	gold quality
right adrenal gland cortex	UBERON:0035827	95.60	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.36	gold quality
endocervix	UBERON:0000458	95.28	gold quality
left adrenal gland cortex	UBERON:0035825	95.17	gold quality
biceps brachii	UBERON:0001507	95.12	gold quality
adrenal cortex	UBERON:0001235	95.08	gold quality
body of uterus	UBERON:0009853	95.08	gold quality
left adrenal gland	UBERON:0001234	95.07	gold quality
lower esophagus	UBERON:0013473	95.05	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.04	gold quality
right adrenal gland	UBERON:0001233	95.03	gold quality
zone of skin	UBERON:0000014	94.90	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.86	gold quality
right atrium auricular region	UBERON:0006631	94.65	gold quality
ganglionic eminence	UBERON:0004023	94.38	gold quality
omental fat pad	UBERON:0010414	94.38	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	140.51
E-MTAB-9467	yes	33.30
E-ANND-3	yes	19.80
E-GEOD-125970	yes	15.89
E-CURD-119	yes	10.14
E-GEOD-130148	yes	5.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

447 targeting C1orf21, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-150-5P	99.99	66.69	1976

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:55943	ENSDARG00000029292
danio_rerio	zgc:92140	ENSDARG00000098592
mus_musculus	1700025G04Rik	ENSMUSG00000032666
rattus_norvegicus	C13h1orf21	ENSRNOG00000028236
drosophila_melanogaster	tow	FBGN0035719
caenorhabditis_elegans		WBGENE00019829

Protein

Protein identifiers

Uncharacterized protein C1orf21 — Q9H246 (reviewed: Q9H246)

Alternative names: Cell proliferation-inducing gene 13 protein

All UniProt accessions (4): Q9H246, A0A3B3ITU3, A0A6Q8PFS2, A0A6Q8PGF2

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in spleen, prostate, testis and uterus.

RefSeq proteins (1): NP_110433* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027967	DUF4612	Family

Pfam: PF15389

UniProt features (5 total): region of interest 2, modified residue 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H246-F1	66.80	0.12

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 (2): 95, 115

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 293 (showing top): RNGTGGGC_UNKNOWN, PAX4_01, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, AAGTCCA_MIR422B_MIR422A, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, BROWNE_HCMV_INFECTION_48HR_DN, AP1_Q4_01, SOX9_B1, AAACCAC_MIR140, TGCTGAY_UNKNOWN, WTGAAAT_UNKNOWN, E4F1_Q6, AAAGACA_MIR511, TGANTCA_AP1_C

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

192 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf21	TMEM131L	A2VDJ0	477
C1orf21	SPPL2C	Q8IUH8	434
C1orf21	NKAPD1	Q6ZUT1	413
C1orf21	ZNF19	P17023	377
C1orf21	RIMOC1	A6NDU8	370
C1orf21	DYNLT4	Q5JR98	370
C1orf21	C10orf71	Q711Q0	370
C1orf21	RNF133	Q8WVZ7	356
C1orf21	SPATA32	Q96LK8	340
C1orf21	APOBEC4	Q8WW27	327
C1orf21	SPAG11A	Q6PDA7	323
C1orf21	EFCAB13	Q8IY85	323
C1orf21	MAGEB18	Q96M61	310
C1orf21	H0YL38	H0YL38	308
C1orf21	ZNF280D	Q6N043	305
C1orf21	TRIM36	Q9NQ86	305

IntAct

22 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
PPP2R5A	C1orf21	psi-mi:“MI:0915”(physical association)	0.670
DRAM1	C1orf21	psi-mi:“MI:0915”(physical association)	0.560
C1orf21	DRAM1	psi-mi:“MI:0915”(physical association)	0.560
TMEM185A	TSPAN6	psi-mi:“MI:0914”(association)	0.530
GJB7	PALM3	psi-mi:“MI:0914”(association)	0.530
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CERS2	VPS37C	psi-mi:“MI:0914”(association)	0.350
MAGEA3	PALM3	psi-mi:“MI:0914”(association)	0.350
CENPM	DNM1L	psi-mi:“MI:0914”(association)	0.350
MTRF1	MEIS1	psi-mi:“MI:0914”(association)	0.350
C1orf21	PPP2R1A	psi-mi:“MI:0914”(association)	0.350
SPATA7	EEPD1	psi-mi:“MI:0914”(association)	0.350
C1orf21	PPP2R1B	psi-mi:“MI:0914”(association)	0.350
KCNK3	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
PPP2R5A	C1orf21	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (44): C1orf21 (Two-hybrid), C1orf21 (Affinity Capture-RNA), C1orf21 (Affinity Capture-RNA), C1orf21 (Affinity Capture-RNA), C1orf21 (Affinity Capture-MS), C1orf21 (Affinity Capture-MS), C1orf21 (Proximity Label-MS), C1orf21 (Synthetic Lethality), C1orf21 (Two-hybrid), C1orf21 (Proximity Label-MS), C1orf21 (Proximity Label-MS), C1orf21 (Proximity Label-MS), C1orf21 (Affinity Capture-MS), C1orf21 (Affinity Capture-RNA), C1orf21 (Proximity Label-MS)

ESM2 similar proteins: A0A088MLT8, B3KU38, B5XE27, O55003, O75391, P04973, P04975, P09496, Q12983, Q15390, Q15650, Q1MSJ5, Q28GU6, Q32KN2, Q3MHJ0, Q3SYW5, Q3ZCD8, Q4KM98, Q4R3X1, Q4R8G4, Q5R795, Q5RD40, Q5RFN3, Q5XG50, Q5XIG4, Q5ZIF8, Q5ZJ97, Q653N3, Q6DC60, Q6DEB4, Q6DGQ4, Q6GQG3, Q6GR00, Q6NVR1, Q6P320, Q6Z746, Q7TNE3, Q7ZXH9, Q8IVM0, Q8IW50

Diamond homologs: Q8K207, Q9H246

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	7
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1809264	GRCh37/hg19 1q25.3-32.3(chr1:181453460-213107248)x3	Pathogenic

SpliceAI

2810 predictions. Top by Δscore:

Variant	Effect	Δscore
1:184427184:TGTAA:T	donor_gain	1.0000
1:184477380:TTGCA:T	acceptor_loss	1.0000
1:184477383:CAGGT:C	acceptor_loss	1.0000
1:184477384:A:AG	acceptor_gain	1.0000
1:184477384:AG:A	acceptor_gain	1.0000
1:184477385:G:GA	acceptor_gain	1.0000
1:184477385:GG:G	acceptor_gain	1.0000
1:184477385:GGT:G	acceptor_gain	1.0000
1:184477600:GGCG:G	donor_gain	1.0000
1:184477601:GCG:G	donor_gain	1.0000
1:184477601:GCGG:G	donor_gain	1.0000
1:184477604:G:GG	donor_gain	1.0000
1:184507578:T:TA	acceptor_gain	1.0000
1:184507579:G:A	acceptor_gain	1.0000
1:184507582:A:AG	acceptor_gain	1.0000
1:184507583:C:G	acceptor_gain	1.0000
1:184507587:GATGA:G	acceptor_gain	1.0000
1:184507679:CTTG:C	donor_gain	1.0000
1:184507679:CTTGG:C	donor_loss	1.0000
1:184507680:TTGGT:T	donor_loss	1.0000
1:184507681:TGGT:T	donor_loss	1.0000
1:184507682:GGT:G	donor_loss	1.0000
1:184507683:G:GG	donor_gain	1.0000
1:184507683:GTAAG:G	donor_loss	1.0000
1:184507684:T:TC	donor_loss	1.0000
1:184529039:A:G	donor_gain	1.0000
1:184590811:GCAAA:G	donor_gain	1.0000
1:184590816:G:GG	donor_gain	1.0000
1:184598395:TTTCA:T	acceptor_loss	1.0000
1:184598397:TCAGC:T	acceptor_loss	1.0000

AlphaMissense

815 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:184598429:T:C	F99L	1.000
1:184598430:T:C	F99S	1.000
1:184598430:T:G	F99C	1.000
1:184598431:C:A	F99L	1.000
1:184598431:C:G	F99L	1.000
1:184598432:T:C	F100L	1.000
1:184598433:T:C	F100S	1.000
1:184598434:C:A	F100L	1.000
1:184598434:C:G	F100L	1.000
1:184598442:T:A	L103Q	1.000
1:184598442:T:C	L103P	1.000
1:184598454:T:A	I107N	1.000
1:184598454:T:G	I107S	1.000
1:184477516:T:C	C3R	0.999
1:184598412:C:T	S93F	0.999
1:184598417:A:C	S95R	0.999
1:184598419:C:A	S95R	0.999
1:184598419:C:G	S95R	0.999
1:184598422:A:C	Q96H	0.999
1:184598422:A:T	Q96H	0.999
1:184598429:T:A	F99I	0.999
1:184598429:T:G	F99V	0.999
1:184598432:T:G	F100V	0.999
1:184598433:T:G	F100C	0.999
1:184598439:T:C	M102T	0.999
1:184598444:G:C	D104H	0.999
1:184598445:A:C	D104A	0.999
1:184598445:A:T	D104V	0.999
1:184598451:A:T	K106I	0.999
1:184598452:A:C	K106N	0.999

dbSNP variants (sampled 300 via entrez): RS1000005984 (1:184551706 C>G,T), RS1000014650 (1:184491466 T>C), RS1000034846 (1:184607031 T>C), RS1000037812 (1:184563608 T>G), RS1000039758 (1:184388196 G>A), RS1000041538 (1:184413706 G>A,T), RS1000045767 (1:184518485 A>G), RS1000063385 (1:184447209 C>G), RS1000063503 (1:184505090 G>A), RS1000082578 (1:184455159 G>T), RS1000086074 (1:184595788 A>C), RS1000086890 (1:184606643 A>C), RS1000099349 (1:184534967 G>A), RS1000113068 (1:184437121 A>G), RS1000134212 (1:184387950 C>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

5 associations (top):

Study	Trait	p-value
GCST006624_35	Systolic blood pressure	7.000000e-15
GCST007267_119	Systolic blood pressure	1.000000e-10
GCST007576_310	Chronotype	1.000000e-08
GCST008403_17	Arterial stiffness index	1.000000e-08
GCST009190_1	Medial orbital frontal cortex volume	4.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0008328	chronotype measurement
EFO:0004517	arterial stiffness measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	4
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	affects methylation, affects cotreatment, decreases expression, increases abundance, increases expression	3
Tretinoin	increases expression, decreases expression	3
Aflatoxin B1	decreases expression, decreases methylation	3
Benzo(a)pyrene	affects methylation, decreases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
FR900359	increases phosphorylation	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	decreases methylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Calcitriol	increases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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