C6orf47

Summary

C6orf47 (chromosome 6 open reading frame 47, HGNC:19076) is a protein-coding gene on chromosome 6p21.33, encoding Uncharacterized protein C6orf47 (O95873).

Predicted to be located in membrane.

Source: NCBI Gene 57827 — RefSeq curated summary.

At a glance

• GWAS associations: 26
• Clinical variants (ClinVar): 3 total — 1 likely-pathogenic
• MANE Select transcript: NM_021184

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19076
Approved symbol	C6orf47
Name	chromosome 6 open reading frame 47
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	D6S53E, G4
Ensembl gene	ENSG00000204439
Ensembl biotype	protein_coding
Entrez	57827

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000375911

RefSeq mRNA: 1 — MANE Select: NM_021184 NM_021184

CCDS: CCDS34399

Canonical transcript exons

ENST00000366431 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 89.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.8019 / max 80.8415, expressed in 1809 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72772	13.8019	1809

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	89.14	gold quality
mucosa of transverse colon	UBERON:0004991	88.91	gold quality
apex of heart	UBERON:0002098	87.69	gold quality
blood	UBERON:0000178	87.33	gold quality
duodenum	UBERON:0002114	86.85	gold quality
lower esophagus mucosa	UBERON:0035834	86.46	gold quality
lower esophagus	UBERON:0013473	86.37	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.37	gold quality
esophagus	UBERON:0001043	86.19	gold quality
esophagus mucosa	UBERON:0002469	86.18	gold quality
transverse colon	UBERON:0001157	85.69	gold quality
leukocyte	CL:0000738	85.68	gold quality
heart left ventricle	UBERON:0002084	85.61	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.55	gold quality
gastrocnemius	UBERON:0001388	85.50	gold quality
monocyte	CL:0000576	85.37	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.34	gold quality
colon	UBERON:0001155	85.22	gold quality
muscle of leg	UBERON:0001383	85.04	gold quality
islet of Langerhans	UBERON:0000006	85.00	gold quality
intestine	UBERON:0000160	84.75	gold quality
urinary bladder	UBERON:0001255	84.65	gold quality
small intestine	UBERON:0002108	84.54	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.52	gold quality
smooth muscle tissue	UBERON:0001135	84.49	gold quality
fundus of stomach	UBERON:0001160	84.41	gold quality
body of stomach	UBERON:0001161	84.36	gold quality
skin of leg	UBERON:0001511	84.21	gold quality
heart	UBERON:0000948	84.15	gold quality
spleen	UBERON:0002106	84.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting C6orf47, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-142-3P	99.62	71.30	974
HSA-MIR-6073	99.60	70.36	793
HSA-MIR-6727-3P	99.49	65.92	1333

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	D17H6S53E	ENSMUSG00000043311
rattus_norvegicus	G4	ENSRNOG00000039658

Protein

Protein identifiers

Uncharacterized protein C6orf47 — O95873 (reviewed: O95873)

Alternative names: Protein G4

All UniProt accessions (2): O95873, A0A1U9X7F2

RefSeq proteins (1): NP_067007* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029073	DUF4661	Family

Pfam: PF15576

UniProt features (13 total): modified residue 4, compositionally biased region 4, region of interest 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95873-F1	57.76	0.00

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 (4): 90, 34, 35, 71

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): AREB6_01, TGACCTY_ERR1_Q2, CACCAGC_MIR138, CAGCTG_AP4_Q5, RYTTCCTG_ETS2_B, TGACCTTG_SF1_Q6, TGGAAA_NFAT_Q4_01, MARSON_BOUND_BY_E2F4_UNSTIMULATED, SCGGAAGY_ELK1_02, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, ERR1_Q2, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CHAF1B_TARGET_GENES, NAB2_TARGET_GENES, SNRNP70_TARGET_GENES

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

370 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C6orf47	GPANK1	O95872	663
C6orf47	LY6G5C	Q5SRR4	568
C6orf47	A0A096LPI6	A0A096LPI6	507
C6orf47	DXO	O77932	487
C6orf47	NELFE	P18615	474
C6orf47	ABHD16A	O95870	474
C6orf47	PRRC2A	P48634	452
C6orf47	PPP1R15A	O75807	419
C6orf47	LSM2	Q9Y333	419
C6orf47	BAG6	P46379	404
C6orf47	CACFD1	Q9UGQ2	392
C6orf47	ZSCAN23	Q3MJ62	390
C6orf47	WHR1	P49842	389
C6orf47	ZBTB12	Q9Y330	387
C6orf47	C1orf35	Q9BU76	383

IntAct

53 interactions, top by confidence:

A	B	Type	Score
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
SLC1A1	AGPAT2	psi-mi:“MI:0914”(association)	0.640
C6orf47	SELENOK	psi-mi:“MI:0915”(physical association)	0.560
C6orf47	RABAC1	psi-mi:“MI:0915”(physical association)	0.560
C6orf47	MEST	psi-mi:“MI:0915”(physical association)	0.560
HTR2C	KLRG2	psi-mi:“MI:0914”(association)	0.530
MAD2L1	PPIP5K2	psi-mi:“MI:0914”(association)	0.530
TACR3	C6orf47	psi-mi:“MI:0914”(association)	0.530
RBM17	C6orf47	psi-mi:“MI:0407”(direct interaction)	0.440
FPR2	GPR89A	psi-mi:“MI:0914”(association)	0.350
rep	B4GALT3	psi-mi:“MI:0914”(association)	0.350
DNAJB6	HSPA8	psi-mi:“MI:0914”(association)	0.350
RTN4	ESYT2	psi-mi:“MI:0914”(association)	0.350
VAPA	ESYT2	psi-mi:“MI:0914”(association)	0.350
VAPB	ESYT2	psi-mi:“MI:0914”(association)	0.350
MAD2L1	MED19	psi-mi:“MI:0914”(association)	0.350
RUSF1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
C5AR1	TCAF2	psi-mi:“MI:0914”(association)	0.350
SEC62	GPR89A	psi-mi:“MI:0914”(association)	0.350
TACR3	TCAF2	psi-mi:“MI:0914”(association)	0.350
ACP2	C6orf47	psi-mi:“MI:0914”(association)	0.350
SEC62	IPO8	psi-mi:“MI:0914”(association)	0.350
ADGRG5	SLC33A1	psi-mi:“MI:0914”(association)	0.350
BSCL2	QSOX1	psi-mi:“MI:0914”(association)	0.350
CCKBR	BTAF1	psi-mi:“MI:0914”(association)	0.350
FZD10	PDE2A	psi-mi:“MI:0914”(association)	0.350
HTR1E	ESYT2	psi-mi:“MI:0914”(association)	0.350
HTR2C	HAT1	psi-mi:“MI:0914”(association)	0.350
S1PR1	ISLR	psi-mi:“MI:0914”(association)	0.350

BioGRID (64): FGFR3 (Two-hybrid), C6orf47 (Affinity Capture-MS), C6orf47 (Affinity Capture-MS), C6orf47 (Proximity Label-MS), C6orf47 (Two-hybrid), C6orf47 (Two-hybrid), C6orf47 (Two-hybrid), C6orf47 (Two-hybrid), C6orf47 (Proximity Label-MS), C6orf47 (Proximity Label-MS), C6orf47 (Proximity Label-MS), C6orf47 (Proximity Label-MS), C6orf47 (Proximity Label-MS), C6orf47 (Proximity Label-MS), C6orf47 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GVZ6, A0A1W2PR82, A0A286YDK6, A2A9F4, A2VE02, A5D7I0, A6H7B4, A6NE82, A6NEV1, A6NJB7, A6NJI1, A6NJJ6, A6QP24, A6QPM6, A8MZG2, D3ZAQ5, D4AAA5, O94850, O95873, P0C7X2, P50617, P70339, Q0P5M0, Q2KIL8, Q2KIS6, Q3UN58, Q3ZCQ2, Q5JPB2, Q5M844, Q5VZ46, Q6AY88, Q6GQX2, Q6NZ36, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86YN6, Q8C1M2, Q8K2F3

Diamond homologs: O95873, Q6MG51, Q9Z1R4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Sphingolipid de novo biosynthesis	5	33.2×	3e-05
SLC-mediated transmembrane transport	6	8.3×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	5	19.5×	7e-04
phospholipase C-activating G protein-coupled receptor signaling pathway	5	11.8×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4538540	NM_021184.4(C6orf47):c.*684_*748del	Likely pathogenic

SpliceAI

84 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31660662:TCGGG:T	donor_gain	0.9400
6:31660659:A:AC	donor_gain	0.7400
6:31660660:C:CC	donor_gain	0.7400
6:31660672:CG:C	donor_gain	0.7300
6:31660662:T:TA	donor_gain	0.7000
6:31660672:CGCGT:C	donor_gain	0.7000
6:31660451:T:TG	acceptor_gain	0.6800
6:31660671:A:AC	donor_gain	0.6700
6:31660672:C:CC	donor_gain	0.6700
6:31660661:TTCGG:T	donor_gain	0.6500
6:31660661:T:C	donor_gain	0.6100
6:31660673:G:C	donor_gain	0.5900
6:31660452:C:A	acceptor_gain	0.5700
6:31659828:T:TA	donor_gain	0.5500
6:31660669:C:T	donor_gain	0.5100
6:31659115:C:G	donor_gain	0.4700
6:31660636:G:C	donor_gain	0.4700
6:31660660:CTTCG:C	donor_gain	0.4500
6:31660620:T:TA	donor_gain	0.4400
6:31660660:CTT:C	donor_gain	0.4200
6:31659116:C:G	donor_gain	0.4100
6:31660657:C:T	donor_gain	0.3900
6:31660524:C:A	donor_gain	0.3700
6:31660676:T:TA	donor_gain	0.3600
6:31660655:G:A	donor_gain	0.3400
6:31659124:T:A	donor_gain	0.3300
6:31660159:C:CC	acceptor_gain	0.3200
6:31660285:T:TC	donor_gain	0.3100
6:31660286:C:CC	donor_gain	0.3100
6:31660287:C:CC	donor_gain	0.3100

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1002270126 (6:31660913 C>G,T), RS1003246539 (6:31660261 G>C), RS1003859566 (6:31657993 C>G,T), RS1005016874 (6:31661876 C>A,G,T), RS1005477810 (6:31658629 C>T), RS1005582024 (6:31662188 G>T), RS1006077512 (6:31661356 C>T), RS1006198971 (6:31658328 G>A,C), RS1006545988 (6:31661671 G>A), RS1007206449 (6:31661037 G>C,T), RS1007246410 (6:31659902 G>A), RS1007603560 (6:31660231 A>C,G), RS1008866963 (6:31661536 A>G), RS1009333846 (6:31661244 G>A), RS1009689066 (6:31661208 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:619735

GenCC curated gene-disease

Mondo (1): spastic paraplegia 86, autosomal recessive (MONDO:0030673)

Orphanet (1): Autosomal recessive spastic paraplegia type 86 (Orphanet:631085)

HPO phenotypes

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

GWAS associations

26 associations (top):

Study	Trait	p-value
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_154	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST004521_17	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_213	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST004521_224	Autism spectrum disorder or schizophrenia	5.000000e-10
GCST004521_227	Autism spectrum disorder or schizophrenia	4.000000e-12
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_281	Autism spectrum disorder or schizophrenia	5.000000e-09
GCST004521_45	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST005006_20	Tuberculosis	2.000000e-12
GCST008916_111	Asthma	2.000000e-14
GCST008916_114	Asthma	1.000000e-09
GCST008916_30	Asthma	1.000000e-09
GCST008917_2	Asthma (childhood onset)	4.000000e-07
GCST008921_1	Asthma and major depressive disorder	2.000000e-16
GCST010725_43	Malaria	5.000000e-07
GCST010725_62	Malaria	3.000000e-06
GCST90002407_248	White blood cell count	3.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008407	susceptibility to Mycobacterium tuberculosis infection measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
2,4,6-tribromophenol	decreases expression	1
bisphenol A	decreases expression	1
decabromobiphenyl ether	decreases expression	1
mono-(2-ethylhexyl)phthalate	decreases methylation, increases abundance	1
tetrabromobisphenol A	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	decreases methylation	1
nickel sulfate	increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	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	increases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Dexamethasone	increases expression, affects cotreatment	1
Diethylhexyl Phthalate	increases abundance, decreases methylation	1
Indomethacin	affects cotreatment, increases expression	1
Niclosamide	affects expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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