C3orf62

Summary

C3orf62 (chromosome 3 open reading frame 62, HGNC:24771) is a protein-coding gene on chromosome 3p21.31, encoding Uncharacterized protein C3orf62 (Q6ZUJ4). Essential for normal spermatogenesis and male fertility.

Predicted to be involved in spermatogenesis.

Source: NCBI Gene 375341 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_198562

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24771
Approved symbol	C3orf62
Name	chromosome 3 open reading frame 62
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43654, MAPS
Ensembl gene	ENSG00000188315
Ensembl biotype	protein_coding
Entrez	375341

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000343010, ENST00000424960, ENST00000436325, ENST00000479673

RefSeq mRNA: 1 — MANE Select: NM_198562 NM_198562

CCDS: CCDS2792

Canonical transcript exons

ENST00000343010 — 3 exons

Exon	Start	End
ENSE00001379253	49276427	49277232
ENSE00001837165	49268596	49271445
ENSE00003568894	49274049	49274140

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 86.22.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1787 / max 51.4237, expressed in 58 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42230	0.0742	15
42231	0.0421	11
42229	0.0312	8
42232	0.0312	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	86.22	gold quality
lower esophagus mucosa	UBERON:0035834	86.07	gold quality
right testis	UBERON:0004534	85.88	gold quality
blood	UBERON:0000178	85.57	gold quality
testis	UBERON:0000473	84.35	gold quality
right adrenal gland cortex	UBERON:0035827	84.09	gold quality
right adrenal gland	UBERON:0001233	83.17	gold quality
granulocyte	CL:0000094	83.07	gold quality
left ovary	UBERON:0002119	82.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.52	gold quality
right ovary	UBERON:0002118	82.29	gold quality
left adrenal gland	UBERON:0001234	81.91	gold quality
left adrenal gland cortex	UBERON:0035825	81.72	gold quality
leukocyte	CL:0000738	81.67	gold quality
monocyte	CL:0000576	81.64	gold quality
apex of heart	UBERON:0002098	81.57	gold quality
adrenal cortex	UBERON:0001235	80.51	gold quality
lower esophagus	UBERON:0013473	80.18	gold quality
lower esophagus muscularis layer	UBERON:0035833	80.17	gold quality
adrenal gland	UBERON:0002369	80.16	gold quality
left uterine tube	UBERON:0001303	80.04	gold quality
spleen	UBERON:0002106	79.36	gold quality
cerebellar hemisphere	UBERON:0002245	79.19	gold quality
cerebellar cortex	UBERON:0002129	79.15	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	78.80	gold quality
omental fat pad	UBERON:0010414	78.62	gold quality
peritoneum	UBERON:0002358	78.56	gold quality
muscle layer of sigmoid colon	UBERON:0035805	78.53	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.50	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.26	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.45
E-MTAB-5061	no	2.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting C3orf62, 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-4795-3P	100.00	74.62	4024
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-3913-3P	99.74	66.53	938
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-6848-3P	99.64	66.49	885
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-330-3P	99.41	69.95	2521

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700102P08Rik	ENSMUSG00000032611
rattus_norvegicus	C8h3orf62	ENSRNOG00000046155

Protein

Protein identifiers

Uncharacterized protein C3orf62 — Q6ZUJ4 (reviewed: Q6ZUJ4)

All UniProt accessions (3): C9JW57, H7BZX3, Q6ZUJ4

UniProt curated annotations — full annotation on UniProt →

Function. Essential for normal spermatogenesis and male fertility.

Tissue specificity. Testis. Down-regulated in men with spermatocyte arrest.

RefSeq proteins (1): NP_940964* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031670	DUF4712	Family

Pfam: PF15830

UniProt features (5 total): modified residue 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUJ4-F1	63.49	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 (2): 210, 224

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, OSMAN_BLADDER_CANCER_DN, TGGAAA_NFAT_Q4_01, SREBP1_Q6, HATADA_METHYLATED_IN_LUNG_CANCER_UP, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, WHITFIELD_CELL_CYCLE_M_G1, BRUINS_UVC_RESPONSE_EARLY_LATE, PKCA_DN.V1_UP, SREBP_Q3, chr3p21, GSE14415_NATURAL_TREG_VS_FOXP3_KO_NATURAL_TREG_DN, ZNF22_TARGET_GENES

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

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
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
binding	1

Protein interactions and networks

STRING

308 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C3orf62	ANKRD65	E5RJM6	479
C3orf62	KNCN	A6PVL3	477
C3orf62	MANSC1	Q9H8J5	452
C3orf62	ZNF570	Q96NI8	447
C3orf62	SUSD6	Q92537	445
C3orf62	OR52B6	Q8NGF0	434
C3orf62	CCDC183	Q5T5S1	431
C3orf62	LSMEM1	Q8N8F7	419
C3orf62	TSEN34	Q9BSV6	409
C3orf62	RNF24	Q9Y225	403
C3orf62	CDHR4	A6H8M9	399
C3orf62	TEX9	Q8N6V9	398
C3orf62	TMCC3	Q9ULS5	396
C3orf62	PLPPR2	Q96GM1	394
C3orf62	ROPN1L	Q96C74	383

IntAct

46 interactions, top by confidence:

A	B	Type	Score
HAUS1	C3orf62	psi-mi:“MI:0915”(physical association)	0.670
MRFAP1L1	C3orf62	psi-mi:“MI:0915”(physical association)	0.670
C3orf62	HAUS1	psi-mi:“MI:0915”(physical association)	0.670
C3orf62	EP300	psi-mi:“MI:2364”(proximity)	0.670
C3orf62	TXNDC9	psi-mi:“MI:0915”(physical association)	0.560
C3orf62	ING5	psi-mi:“MI:0915”(physical association)	0.560
C3orf62	MRFAP1	psi-mi:“MI:0915”(physical association)	0.560
ING5	C3orf62	psi-mi:“MI:0915”(physical association)	0.560
MRFAP1	C3orf62	psi-mi:“MI:0915”(physical association)	0.560
KRT3	C3orf62	psi-mi:“MI:0915”(physical association)	0.560
RFPL3	C3orf62	psi-mi:“MI:0915”(physical association)	0.560
BFSP2	C3orf62	psi-mi:“MI:0915”(physical association)	0.560
C3orf62	LMNTD2	psi-mi:“MI:0915”(physical association)	0.560
C3orf62	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
C3orf62	RB1	psi-mi:“MI:0914”(association)	0.530
DGCR6	C3orf62	psi-mi:“MI:0915”(physical association)	0.370
C3orf62	ALDH1L1	psi-mi:“MI:0914”(association)	0.350
C3orf62	SCO1	psi-mi:“MI:0914”(association)	0.350

BioGRID (43): C3orf62 (Two-hybrid), C3orf62 (Two-hybrid), C3orf62 (Two-hybrid), C3orf62 (Two-hybrid), C3orf62 (Two-hybrid), CREBBP (Affinity Capture-MS), EP300 (Affinity Capture-MS), RB1 (Affinity Capture-MS), RBL1 (Affinity Capture-MS), C3orf62 (Two-hybrid), EP300 (Affinity Capture-MS), CREBBP (Affinity Capture-MS), RBL1 (Affinity Capture-MS), RB1 (Affinity Capture-MS), C3orf62 (Two-hybrid)

ESM2 similar proteins: A0A0B4J1W7, A0A1B0GUC4, A4GZ95, A6NHN6, A6NJ64, A6ZT44, A8MTZ7, E9PJ23, E9PJI5, E9PKD4, E9PQR5, F8W1W9, F8WFD2, O75200, O91083, P04605, P05909, P05910, P05911, P0DM63, P0DXC3, P12453, P12513, P17759, P18044, P18098, P19507, P20880, P38839, P38900, Q02838, Q1KN10, Q1KN16, Q1KN23, Q1X6Y7, Q1X6Z0, Q1X6Z2, Q1X6Z3, Q2YDP6, Q32LJ5

Diamond homologs: Q6ZUJ4, Q9D9C7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

7 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	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

548 predictions. Top by Δscore:

Variant	Effect	Δscore
3:49271447:T:C	acceptor_gain	1.0000
3:49274150:CCAGG:C	acceptor_gain	1.0000
3:49274151:C:T	acceptor_gain	1.0000
3:49274151:CAGG:C	acceptor_gain	1.0000
3:49274152:A:T	acceptor_gain	1.0000
3:49271446:C:CC	acceptor_gain	0.9900
3:49271447:T:TC	acceptor_gain	0.9900
3:49274154:G:C	acceptor_gain	0.9900
3:49274154:G:GC	acceptor_gain	0.9900
3:49271442:TGGT:T	acceptor_gain	0.9800
3:49274138:TTC:T	acceptor_gain	0.9800
3:49271443:GGTC:G	acceptor_loss	0.9600
3:49271444:GTC:G	acceptor_loss	0.9600
3:49271445:TCT:T	acceptor_loss	0.9600
3:49271446:CTTAA:C	acceptor_loss	0.9600
3:49274136:CTTTC:C	acceptor_gain	0.9600
3:49277173:T:TA	donor_gain	0.9600
3:49271443:GGT:G	acceptor_gain	0.9500
3:49271444:GT:G	acceptor_gain	0.9500
3:49271444:GTCTT:G	acceptor_gain	0.9500
3:49271453:A:C	acceptor_loss	0.9500
3:49274048:CCAAT:C	donor_gain	0.9500
3:49274139:TC:T	acceptor_gain	0.9500
3:49274140:CC:C	acceptor_gain	0.9500
3:49274141:C:CC	acceptor_gain	0.9400
3:49274139:TCCTG:T	acceptor_loss	0.9300
3:49274140:CCTGC:C	acceptor_loss	0.9300
3:49274142:T:A	acceptor_loss	0.9300
3:49274040:TGTAC:T	donor_loss	0.9200
3:49274041:GTAC:G	donor_loss	0.9200

AlphaMissense

1778 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:49276802:A:G	L24P	0.995
3:49276794:C:G	A27P	0.992
3:49271238:A:T	V249D	0.991
3:49276810:T:A	R21S	0.990
3:49276810:T:G	R21S	0.990
3:49276811:C:A	R21I	0.986
3:49276811:C:G	R21T	0.986
3:49276784:C:G	R30P	0.984
3:49276802:A:T	L24Q	0.984
3:49276823:A:G	L17P	0.984
3:49276790:A:T	I28N	0.982
3:49276797:C:G	A26P	0.980
3:49271235:A:G	L250P	0.978
3:49276793:G:T	A27D	0.978
3:49276782:C:G	A31P	0.973
3:49276815:A:G	C20R	0.973
3:49276834:C:A	M13I	0.972
3:49276834:C:G	M13I	0.972
3:49276834:C:T	M13I	0.972
3:49276790:A:C	I28S	0.969
3:49271415:A:G	L190S	0.964
3:49276832:G:A	S14F	0.963
3:49276781:G:T	A31D	0.961
3:49276802:A:C	L24R	0.961
3:49276812:T:C	R21G	0.961
3:49276813:G:C	C20W	0.961
3:49271225:T:A	E253D	0.960
3:49271225:T:G	E253D	0.960
3:49271229:A:G	L252S	0.955
3:49276823:A:T	L17Q	0.955

dbSNP variants (sampled 300 via entrez): RS1000050116 (3:49275429 T>G), RS1000222645 (3:49275693 G>A), RS1000272501 (3:49268174 C>T), RS1000403796 (3:49275720 C>CA), RS1000759051 (3:49274555 C>G,T), RS1001009254 (3:49274054 A>G), RS1001226706 (3:49276937 C>T), RS1001332877 (3:49276355 G>A), RS1001466873 (3:49276652 G>T), RS1001560603 (3:49274901 C>T), RS1002053755 (3:49274534 TA>T), RS1002658381 (3:49273169 A>C,G), RS1003017178 (3:49273432 A>G), RS1003337175 (3:49278688 GCT>G), RS1003536083 (3:49271693 G>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

10 associations (top):

Study	Trait	p-value
GCST004131_23	Inflammatory bowel disease	1.000000e-33
GCST004132_17	Crohn’s disease	3.000000e-23
GCST004133_11	Ulcerative colitis	8.000000e-20
GCST004621_57	Red cell distribution width	9.000000e-10
GCST010698_80	Subcortical volume (min-P)	3.000000e-24
GCST010699_110	Brain morphology (min-P)	4.000000e-08
GCST010701_52	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_36	Subcortical volume (MOSTest)	1.000000e-10
GCST010703_262	Brain morphology (MOSTest)	2.000000e-13
GCST012355_28	Depression	2.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Ozone	affects expression, increases abundance, decreases expression	2
Valproic Acid	affects cotreatment, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
2-palmitoylglycerol	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	decreases expression, affects reaction	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Demecolcine	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	increases expression	1
Lactic Acid	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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