C5orf58

Summary

C5orf58 (chromosome 5 open reading frame 58, HGNC:37272) is a protein-coding gene on chromosome 5q35.1, encoding Putative uncharacterized protein C5orf58 (C9J3I9).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 26 total — 2 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_001102609

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37272
Approved symbol	C5orf58
Name	chromosome 5 open reading frame 58
Location	5q35.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000234511
Ensembl biotype	protein_coding
Entrez	133874

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 retained_intron

ENST00000421269, ENST00000517575, ENST00000518395, ENST00000521850, ENST00000524171, ENST00000593851, ENST00000706941, ENST00000919417, ENST00000919418

RefSeq mRNA: 3 — MANE Select: NM_001102609 NM_001102609, NM_001305393, NM_001305394

CCDS: CCDS47338

Canonical transcript exons

ENST00000593851 — 4 exons

Exon	Start	End
ENSE00002994840	170245962	170246231
ENSE00003682619	170234977	170235070
ENSE00003997549	170234115	170234198
ENSE00003997550	170232985	170233007

Expression profiles

Bgee: expression breadth ubiquitous, 155 present calls, max score 99.29.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3214 / max 222.8360, expressed in 48 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60105	0.2893	46
60106	0.0321	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	99.29	gold quality
left testis	UBERON:0004533	99.06	gold quality
sperm	CL:0000019	97.72	gold quality
testis	UBERON:0000473	97.00	gold quality
adult organism	UBERON:0007023	96.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.74	gold quality
oocyte	CL:0000023	91.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.10	gold quality
secondary oocyte	CL:0000655	85.38	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.57	gold quality
spinal cord	UBERON:0002240	78.36	gold quality
granulocyte	CL:0000094	78.32	gold quality
monocyte	CL:0000576	77.69	gold quality
leukocyte	CL:0000738	77.24	gold quality
blood	UBERON:0000178	73.70	gold quality
bone marrow cell	CL:0002092	72.87	gold quality
vermiform appendix	UBERON:0001154	69.69	gold quality
spleen	UBERON:0002106	69.45	gold quality
subcutaneous adipose tissue	UBERON:0002190	69.31	gold quality
minor salivary gland	UBERON:0001830	69.26	gold quality
upper lobe of left lung	UBERON:0008952	68.42	gold quality
omental fat pad	UBERON:0010414	68.09	gold quality
peritoneum	UBERON:0002358	68.02	gold quality
upper lobe of lung	UBERON:0008948	67.68	gold quality
right coronary artery	UBERON:0001625	67.33	gold quality
colonic epithelium	UBERON:0000397	67.29	silver quality
adipose tissue of abdominal region	UBERON:0007808	66.59	gold quality
tibial nerve	UBERON:0001323	66.50	gold quality
endocervix	UBERON:0000458	66.05	gold quality
mouth mucosa	UBERON:0003729	65.73	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	1725.77
E-ANND-3	yes	4.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting C5orf58, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-5000-5P	97.40	66.11	1055

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Putative uncharacterized protein C5orf58 — C9J3I9 (reviewed: C9J3I9)

All UniProt accessions (4): C9J3I9, A0A1B0GVU6, A0A2R8Y5L7, A0A9L9PY61

RefSeq proteins (3): NP_001096079, NP_001292322, NP_001292323 (=MANE)

Domains & families (InterPro)

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9J3I9-F1	76.46	0.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): PAX3_TARGET_GENES, LET_7A_3P, MIR98_3P, LET_7F_1_3P, LET_7B_3P, GSE11057_NAIVE_VS_CENT_MEMORY_CD4_TCELL_UP, MIR150_5P, GSE13485_CTRL_VS_DAY1_YF17D_VACCINE_PBMC_DN, GSE13485_DAY1_VS_DAY3_YF17D_VACCINE_PBMC_UP, SMN1_SMN2_TARGET_GENES, DESCARTES_MAIN_FETAL_MEGAKARYOCYTES, MYBL1_TARGET_GENES, HOWARD_DENDRITIC_CELL_INACT_MONOV_INFLUENZA_A_INDONESIA_05_2005_H5N1_AGE_18_49YO_1DY_UP, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_UP, GSE4748_LPS_VS_LPS_AND_CYANOBACTERIUM_LPSLIKE_STIM_DC_3H_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

94 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C5orf58	UBTD2	Q8WUN7	520
C5orf58	HEATR9	A2RTY3	507
C5orf58	GTSF1L	Q9H1H1	503
C5orf58	TM6SF2	Q9BZW4	473
C5orf58	HAPLN4	Q86UW8	468
C5orf58	TSSK6	Q9BXA6	447
C5orf58	ZNF101	Q8IZC7	433
C5orf58	KCNIP1	Q9NZI2	428
C5orf58	CILP2	Q8IUL8	423
C5orf58	HSF5	Q4G112	418
C5orf58	SH3PXD2B	A1X283	392
C5orf58	CLEC16A	Q2KHT3	375
C5orf58	KLHL14	Q9P2G3	371
C5orf58	TMCO4	Q5TGY1	364
C5orf58	ZDBF2	Q9HCK1	348

IntAct

2 interactions, top by confidence:

A	B	Type	Score
C5orf58	EIF3I	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): EIF3I (Proximity Label-MS)

ESM2 similar proteins: A4ZU97, A6Q1W8, A6ZS79, B0BCM0, B3LPN5, B5F9X9, B8E1C2, C0H3W7, C5BHB2, C5D5A9, C7GLQ0, C8ZFN1, C9J3I9, D1AZF3, O29520, O50843, P07616, P09521, P0CAN3, P0CAN4, P0CAN5, P0CE23, P15915, P21032, P33004, P40342, P64665, P64666, P75248, Q06423, Q28ZG0, Q2SPM9, Q3M644, Q3V4Q2, Q44149, Q46262, Q46440, Q57734, Q58645, Q5BKH4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	13
Likely benign	3
Benign	2

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
2425244	NC_000005.9:g.(?167849013)(169661202_?)del	Pathogenic
3062837	GRCh37/hg19 5q34-35.1(chr5:165763259-170909410)x1	Pathogenic
980751	GRCh37/hg19 5q34-35.1(chr5:166378793-170174830)x1	Likely pathogenic

SpliceAI

248 predictions. Top by Δscore:

Variant	Effect	Δscore
5:170250724:CCTTA:C	donor_loss	1.0000
5:170250725:CTTAC:C	donor_loss	1.0000
5:170250726:TTACC:T	donor_loss	1.0000
5:170250727:TACC:T	donor_loss	1.0000
5:170250728:A:AC	donor_gain	1.0000
5:170250728:ACCTC:A	donor_loss	1.0000
5:170250729:C:A	donor_loss	1.0000
5:170250729:C:CC	donor_gain	1.0000
5:170250729:CCT:C	donor_gain	1.0000
5:170250773:T:A	donor_gain	1.0000
5:170250881:CCATC:C	acceptor_gain	1.0000
5:170250882:CATC:C	acceptor_gain	1.0000
5:170250882:CATCC:C	acceptor_gain	1.0000
5:170250884:TC:T	acceptor_gain	1.0000
5:170250884:TCC:T	acceptor_loss	1.0000
5:170250885:CC:C	acceptor_gain	1.0000
5:170250886:C:CC	acceptor_gain	1.0000
5:170250886:CTAAA:C	acceptor_loss	1.0000
5:170250887:T:A	acceptor_loss	1.0000
5:170250883:ATC:A	acceptor_gain	0.9900
5:170250886:C:T	acceptor_gain	0.9900
5:170248929:T:TC	acceptor_gain	0.9700
5:170250886:CTAA:C	acceptor_gain	0.9600
5:170252510:TT:T	acceptor_gain	0.9600
5:170250823:C:CT	acceptor_gain	0.9500
5:170252512:C:CC	acceptor_gain	0.9500
5:170248820:C:CC	acceptor_gain	0.9400
5:170250728:ACCT:A	donor_gain	0.9300
5:170250729:CCTC:C	donor_gain	0.9300
5:170246666:C:T	acceptor_gain	0.9200

AlphaMissense

538 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000016857 (5:170239732 A>G), RS1000233765 (5:170232094 G>A,T), RS1000262893 (5:170236051 C>A), RS1000574461 (5:170246360 T>C), RS1000698290 (5:170236470 C>T), RS1000708904 (5:170247749 A>G), RS1000900845 (5:170238379 G>A), RS1001326799 (5:170248140 ATAAAAAAATTAC>A), RS1001682326 (5:170233104 C>T), RS1001855076 (5:170247495 G>A,T), RS1002308901 (5:170248686 G>C), RS1002371151 (5:170247202 C>G,T), RS1002455068 (5:170238796 A>G), RS1002576399 (5:170243171 A>G), RS1002641751 (5:170231855 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:616433, MIM:619374

GenCC curated gene-disease

Mondo (2): DOCK2 deficiency (MONDO:0014637), immunodeficiency 81 (MONDO:0030302)

Orphanet (1): Combined immunodeficiency due to DOCK2 deficiency (Orphanet:447737)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002481_3	Acne (severe)	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression, increases methylation	3
Nickel	increases expression	2
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cupric oxide	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
di-n-butylphosphoric acid	affects expression	1
Arsenic Trioxide	decreases expression	1
Folic Acid	decreases expression	1
Lead	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Phthalic Acids	decreases methylation	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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