C6orf62

Summary

C6orf62 (chromosome 6 open reading frame 62, HGNC:20998) is a protein-coding gene on chromosome 6p22.3, encoding Uncharacterized protein C6orf62 (Q9GZU0).

At a glance

• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_030939

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20998
Approved symbol	C6orf62
Name	chromosome 6 open reading frame 62
Location	6p22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12619, DKFZP564G182, XTP12
Ensembl gene	ENSG00000112308
Ensembl biotype	protein_coding
Entrez	81688

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000378102, ENST00000378119, ENST00000710317, ENST00000853645, ENST00000853646, ENST00000853647, ENST00000853648, ENST00000853649, ENST00000853650, ENST00000927908, ENST00000966687

RefSeq mRNA: 2 — MANE Select: NM_030939 NM_001410835, NM_030939

CCDS: CCDS4559, CCDS93869

Canonical transcript exons

ENST00000378119 — 5 exons

Exon	Start	End
ENSE00000693550	24714318	24714440
ENSE00001174654	24704861	24706262
ENSE00001476498	24718540	24719154
ENSE00003393005	24708777	24708911
ENSE00003472602	24716148	24716324

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 98.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 266.7781 / max 22629.5065, expressed in 1828 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72207	120.0645	1827
72202	108.0460	1813
72208	24.5589	1815
72209	9.3421	1767
72203	2.2873	1281
72206	1.7932	889
72204	0.6410	339
72205	0.0452	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pylorus	UBERON:0001166	98.72	gold quality
monocyte	CL:0000576	98.58	gold quality
mononuclear cell	CL:0000842	98.53	gold quality
leukocyte	CL:0000738	98.51	gold quality
palpebral conjunctiva	UBERON:0001812	98.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	98.46	gold quality
germinal epithelium of ovary	UBERON:0001304	98.40	gold quality
superior vestibular nucleus	UBERON:0007227	98.24	gold quality
body of pancreas	UBERON:0001150	98.22	gold quality
cardia of stomach	UBERON:0001162	98.19	gold quality
lymph node	UBERON:0000029	98.14	gold quality
trigeminal ganglion	UBERON:0001675	98.13	gold quality
ganglionic eminence	UBERON:0004023	98.13	gold quality
inferior vagus X ganglion	UBERON:0005363	98.01	gold quality
medial globus pallidus	UBERON:0002477	98.00	gold quality
pericardium	UBERON:0002407	97.99	gold quality
ventricular zone	UBERON:0003053	97.97	gold quality
globus pallidus	UBERON:0001875	97.95	gold quality
substantia nigra pars reticulata	UBERON:0001966	97.95	gold quality
right testis	UBERON:0004534	97.94	gold quality
amniotic fluid	UBERON:0000173	97.92	gold quality
endometrium	UBERON:0001295	97.91	gold quality
granulocyte	CL:0000094	97.90	gold quality
substantia nigra pars compacta	UBERON:0001965	97.85	gold quality
parietal pleura	UBERON:0002400	97.81	gold quality
cortical plate	UBERON:0005343	97.80	gold quality
testis	UBERON:0000473	97.79	gold quality
stromal cell of endometrium	CL:0002255	97.76	gold quality
spleen	UBERON:0002106	97.75	gold quality
superior surface of tongue	UBERON:0007371	97.72	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-8498	yes	8.72
E-GEOD-70580	no	3098.76
E-MTAB-6819	no	1910.77
E-CURD-89	no	1284.96
E-MTAB-10137	no	649.65
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

139 targeting C6orf62, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	C19H6orf62	ENSDARG00000093406
mus_musculus	BC005537	ENSMUSG00000019132
rattus_norvegicus	C17h6orf62	ENSRNOG00000018456

Protein

Protein identifiers

Uncharacterized protein C6orf62 — Q9GZU0 (reviewed: Q9GZU0)

Alternative names: HBV X-transactivated gene 12 protein, HBV XAg-transactivated protein 12

All UniProt accessions (1): Q9GZU0

Isoforms (2)

UniProt ID	Names	Canonical?
Q9GZU0-1	1	yes
Q9GZU0-2	2

RefSeq proteins (2): NP_001397764, NP_112201* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027903	C6orf62	Domain

Pfam: PF15130

UniProt features (6 total): splice variant 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9GZU0-F1	83.38	0.46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 257 (showing top): RNGTGGGC_UNKNOWN, MYAATNNNNNNNGGC_UNKNOWN, MORF_RAD21, MORF_HDAC2, AP2_Q3, MORF_PSMC2, CAGCTG_AP4_Q5, GATA1_01, HEN1_01, WTGAAAT_UNKNOWN, TCF11_01, E4F1_Q6, NRF2_Q4, NKX22_01, AFP1_Q6

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (0):

Protein interactions and networks

STRING

338 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C6orf62	ACOT13	Q9NPJ3	475
C6orf62	DHX29	Q7Z478	456
C6orf62	KAAG1	Q9UBP8	446
C6orf62	KIAA0319	Q5VV43	446
C6orf62	TAF6	P49848	445
C6orf62	ITPA	Q9BY32	438
C6orf62	TRIP6	Q15654	433
C6orf62	RIPOR2	Q9Y4F9	431
C6orf62	RUSF1	Q96GQ5	419
C6orf62	KIF1B	O60333	413
C6orf62	ATP1A2	P50993	410
C6orf62	NRSN1	Q8IZ57	399
C6orf62	MAP4K4	O95819	398
C6orf62	KIF2C	Q99661	398
C6orf62	JARID2	Q92833	391

IntAct

8 interactions, top by confidence:

A	B	Type	Score
COX5B	COX7A2L	psi-mi:“MI:0914”(association)	0.530
NECTIN4	EIF2B2	psi-mi:“MI:0914”(association)	0.530
C6orf62	HAL	psi-mi:“MI:0915”(physical association)	0.400
SLC22A4	RTL8C	psi-mi:“MI:0914”(association)	0.350
C6orf62	MAP2K7	psi-mi:“MI:0914”(association)	0.350
NDUFA4L2	C6orf62	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): C6orf62 (Affinity Capture-MS), C6orf62 (Affinity Capture-MS), C6orf62 (Affinity Capture-MS), FDX1L (Affinity Capture-MS), VPS36 (Affinity Capture-MS), C6orf62 (Affinity Capture-MS), UBE4A (Affinity Capture-MS), SNF8 (Affinity Capture-MS), C6orf62 (Affinity Capture-MS), VPS25 (Affinity Capture-MS), PNKP (Affinity Capture-MS), MAP2K7 (Affinity Capture-MS), ASUN (Affinity Capture-MS), XRCC1 (Affinity Capture-MS), ASB6 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8H579, A0A1P8ARG1, A0A3B7TNW2, A1XIQ0, A2XTW9, A3CEM4, B2ZCQ2, B2ZCQ3, C6EN00, F4I1X0, F5HAI6, I1R9B4, I6LJ77, O36416, O76616, O96624, P09003, P09004, P0DUE1, P11468, P15718, P21299, P29476, P40587, Q02330, Q06003, Q20A00, Q23376, Q2QYR5, Q32L96, Q39072, Q3E8K6, Q58FY4, Q5R4W4, Q66WT5, Q6AYN4, Q7X9V2, Q89759, Q8BGT8, Q8H6Z6

Diamond homologs: Q5R4W4, Q99LU8, Q9GZU0

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	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1034 predictions. Top by Δscore:

Variant	Effect	Δscore
6:24708772:CTTA:C	donor_loss	1.0000
6:24708775:A:AC	donor_gain	1.0000
6:24708776:C:A	donor_loss	1.0000
6:24708776:C:CC	donor_gain	1.0000
6:24708776:CCTG:C	donor_gain	1.0000
6:24708912:C:CC	acceptor_gain	1.0000
6:24708913:T:A	acceptor_loss	1.0000
6:24708916:T:C	acceptor_gain	1.0000
6:24708916:T:TC	acceptor_gain	1.0000
6:24709707:C:CA	donor_gain	1.0000
6:24716143:CTTA:C	donor_loss	1.0000
6:24716144:TTACC:T	donor_loss	1.0000
6:24716145:TACC:T	donor_loss	1.0000
6:24716146:A:AC	donor_gain	1.0000
6:24716146:AC:A	donor_gain	1.0000
6:24716146:ACC:A	donor_gain	1.0000
6:24716146:ACCC:A	donor_loss	1.0000
6:24716147:C:CT	donor_gain	1.0000
6:24716147:CC:C	donor_gain	1.0000
6:24716147:CCC:C	donor_gain	1.0000
6:24716147:CCCT:C	donor_gain	1.0000
6:24716147:CCCTT:C	donor_gain	1.0000
6:24716320:TTCTT:T	acceptor_gain	1.0000
6:24716321:TCTTC:T	acceptor_gain	1.0000
6:24716322:CTT:C	acceptor_gain	1.0000
6:24716322:CTTCT:C	acceptor_gain	1.0000
6:24716323:TT:T	acceptor_gain	1.0000
6:24716324:TC:T	acceptor_loss	1.0000
6:24716325:C:CC	acceptor_gain	1.0000
6:24716325:CTA:C	acceptor_loss	1.0000

AlphaMissense

1532 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:24716179:A:G	L92P	1.000
6:24706210:A:G	L206P	0.999
6:24714371:A:G	C126R	0.999
6:24716165:A:C	Y97D	0.999
6:24716173:G:T	A94D	0.999
6:24718580:A:G	F30S	0.999
6:24706187:A:G	W214R	0.998
6:24706187:A:T	W214R	0.998
6:24706195:A:G	L211P	0.998
6:24706216:A:G	L204P	0.998
6:24706218:G:C	C203W	0.998
6:24706220:A:G	C203R	0.998
6:24708802:A:G	L180P	0.998
6:24708804:A:C	F179L	0.998
6:24708804:A:T	F179L	0.998
6:24708806:A:G	F179L	0.998
6:24714322:A:T	V142D	0.998
6:24714353:A:G	W132R	0.998
6:24714353:A:T	W132R	0.998
6:24714401:A:G	W116R	0.998
6:24714401:A:T	W116R	0.998
6:24714409:A:G	F113S	0.998
6:24716185:A:T	V90E	0.998
6:24716203:A:G	L84P	0.998
6:24716281:A:T	V58D	0.998
6:24716290:A:T	V55D	0.998
6:24716305:A:G	F50S	0.998
6:24718559:G:T	A37D	0.998
6:24718579:A:C	F30L	0.998
6:24718579:A:T	F30L	0.998

dbSNP variants (sampled 300 via entrez): RS1000037437 (6:24719046 A>G), RS1000086319 (6:24708332 G>A), RS1000099569 (6:24712177 G>C), RS1000377376 (6:24715113 G>A), RS1000518978 (6:24708292 T>C), RS1000713728 (6:24712489 T>C), RS1000769449 (6:24714766 C>T), RS1000786384 (6:24718978 T>A,G), RS1000840122 (6:24719299 T>C), RS1000971025 (6:24718097 G>A,C,T), RS1001116034 (6:24713558 T>G), RS1001408213 (6:24720857 A>C), RS1001437756 (6:24720797 G>A), RS1001570357 (6:24716849 G>A,C), RS1001716151 (6:24711353 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases methylation	2
Air Pollutants	decreases expression, affects expression, increases abundance	2
Formaldehyde	increases expression	2
Hydrogen Peroxide	affects expression, decreases expression	2
Tobacco Smoke Pollution	increases expression, increases methylation	2
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
abrine	increases expression	1
jinfukang	decreases expression	1
Bortezomib	increases expression	1
Resveratrol	increases expression, affects cotreatment	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Arsenic	affects expression	1
Azacitidine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Doxorubicin	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	increases expression	1
Silicon Dioxide	decreases expression	1
Thiram	decreases expression	1
Tretinoin	increases expression	1
Urethane	increases expression	1
Valproic Acid	affects expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1LU	Abcam HeLa C6orf62 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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