C6orf52

Summary

C6orf52 (chromosome 6 open reading frame 52, HGNC:20881) is a protein-coding gene on chromosome 6p24.2, encoding Putative uncharacterized protein C6orf52 (Q5T4I8).

At a glance

• Clinical variants (ClinVar): 18 total — 1 pathogenic
• MANE Select transcript: NM_001145020

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20881
Approved symbol	C6orf52
Name	chromosome 6 open reading frame 52
Location	6p24.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000137434
Ensembl biotype	protein_coding
OMIM	621281
Entrez	347744

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000259983, ENST00000379586, ENST00000426700, ENST00000460742, ENST00000467832, ENST00000503680, ENST00000896013

RefSeq mRNA: 4 — MANE Select: NM_001145020 NM_001145020, NM_001354357, NM_001388310, NM_001388311

CCDS: CCDS47371, CCDS87364

Canonical transcript exons

ENST00000259983 — 5 exons

Exon	Start	End
ENSE00001734482	10694494	10694616
ENSE00003484752	10687480	10687561
ENSE00003491086	10671422	10671598
ENSE00003565228	10683187	10683232
ENSE00003619761	10686966	10687164

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 90.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.5596 / max 54.1666, expressed in 1090 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
71694	2.5596	1090

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.60	gold quality
right testis	UBERON:0004534	83.37	gold quality
testis	UBERON:0000473	82.89	gold quality
left testis	UBERON:0004533	82.60	gold quality
right uterine tube	UBERON:0001302	81.41	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.63	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	80.37	gold quality
duodenum	UBERON:0002114	77.61	gold quality
islet of Langerhans	UBERON:0000006	75.72	gold quality
ganglionic eminence	UBERON:0004023	72.81	gold quality
hypothalamus	UBERON:0001898	72.70	gold quality
amygdala	UBERON:0001876	71.56	gold quality
substantia nigra	UBERON:0002038	71.53	gold quality
temporal lobe	UBERON:0001871	71.44	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	71.40	gold quality
Ammon’s horn	UBERON:0001954	70.60	gold quality
prostate gland	UBERON:0002367	70.07	gold quality
pancreas	UBERON:0001264	69.66	gold quality
right adrenal gland cortex	UBERON:0035827	69.52	gold quality
stromal cell of endometrium	CL:0002255	69.27	gold quality
anterior cingulate cortex	UBERON:0009835	69.18	gold quality
prefrontal cortex	UBERON:0000451	69.16	gold quality
primary visual cortex	UBERON:0002436	69.10	gold quality
right adrenal gland	UBERON:0001233	68.83	gold quality
endometrium	UBERON:0001295	68.83	gold quality
nucleus accumbens	UBERON:0001882	68.63	gold quality
ventricular zone	UBERON:0003053	68.55	gold quality
left adrenal gland cortex	UBERON:0035825	68.48	gold quality
cerebral cortex	UBERON:0000956	68.47	gold quality
caudate nucleus	UBERON:0001873	68.20	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	22.05
E-ANND-3	no	2.51

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	C17h6orf52	ENSRNOG00000039379

Protein

Protein identifiers

Putative uncharacterized protein C6orf52 — Q5T4I8 (reviewed: Q5T4I8)

All UniProt accessions (3): Q5T4I8, D6RAP8, D6RGE8

Isoforms (2)

UniProt ID	Names	Canonical?
Q5T4I8-1	1	yes
Q5T4I8-2	2

RefSeq proteins (4): NP_001138492, NP_001341286, NP_001375239, NP_001375240 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040434	TSAP1	Family
IPR041085	TSAP1_C	Domain

Pfam: PF17654

UniProt features (3 total): chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T4I8-F1	58.15	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, chr6p24, KOYAMA_SEMA3B_TARGETS_DN, STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN, JOHNSTONE_PARVB_TARGETS_3_DN, BARX1_TARGET_GENES, DACH1_TARGET_GENES, DIDO1_TARGET_GENES, E2F2_TARGET_GENES, FEV_TARGET_GENES, IRF5_TARGET_GENES, KLF7_TARGET_GENES, NCOA2_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1219 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C6orf52	CENATAC	Q86UT8	613
C6orf52	RBM44	Q6ZP01	507
C6orf52	IMPG1	Q17R60	504
C6orf52	TOR1AIP2	Q8NFQ8	484
C6orf52	WAC	Q9BTA9	431
C6orf52	ASMTL	O95671	411
C6orf52	GABRR1	P24046	411
C6orf52	TMSB15A	P0CG34	377
C6orf52	LCA5	Q86VQ0	366
C6orf52	EEFSEC	P57772	348
C6orf52	SEPSECS	Q9HD40	348
C6orf52	AMPD3	Q01432	346
C6orf52	PRPF39	Q86UA1	340
C6orf52	ELOVL4	Q9GZR5	334
C6orf52	MYO6	Q9UM54	329

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A345BJN6, B3FWS0, C9K7C3, G1XTZ6, G4NB33, I1S490, K0DZ91, K3VDP7, O09102, O15198, O36398, O75603, O93958, P09265, P09286, P0CK38, P13622, P17924, P17926, P21944, P24433, P28937, P28989, P35192, P36280, P68349, P68948, P68949, P70255, P70348, P80074, P9WEJ9, Q00028, Q06658, Q08427, Q08589, Q2U9L6, Q4JQW5, Q4QFD3, Q5T4I8

Diamond homologs: A2VDB3, F4I3B3, O13759, O22173, O57437, O60176, P08199, P09405, P0CB38, P13383, P19338, P32588, P39697, P41891, P70318, Q00539, Q01085, Q0J9Y2, Q0P5L0, Q0WW84, Q10355, Q15427, Q1RMJ7, Q24207, Q4KM14, Q4R4J7, Q4V7Y4, Q503H1, Q5R462, Q5RF26, Q5T4I8, Q64368, Q66J99, Q66KL9, Q6AXT7, Q6AYL5, Q6DRG1, Q6YZW2, Q76CY5, Q804A9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	13
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
146906	GRCh38/hg38 6p25.2-24.1(chr6:4068792-13267799)x1	Pathogenic

SpliceAI

877 predictions. Top by Δscore:

Variant	Effect	Δscore
6:10671609:C:CT	acceptor_gain	1.0000
6:10671610:A:T	acceptor_gain	1.0000
6:10671608:CCAA:C	acceptor_gain	0.9900
6:10671609:C:T	acceptor_gain	0.9900
6:10671611:A:AC	acceptor_gain	0.9900
6:10671596:GATC:G	acceptor_loss	0.9800
6:10671597:ATCT:A	acceptor_loss	0.9800
6:10671598:TC:T	acceptor_loss	0.9800
6:10671599:C:CC	acceptor_gain	0.9800
6:10671611:A:C	acceptor_gain	0.9800
6:10671614:A:C	acceptor_gain	0.9800
6:10671620:A:C	acceptor_gain	0.9800
6:10694492:AC:A	donor_gain	0.9800
6:10694493:CC:C	donor_gain	0.9800
6:10671594:TGGAT:T	acceptor_gain	0.9700
6:10671609:CAA:C	acceptor_loss	0.9700
6:10671614:A:AC	acceptor_gain	0.9700
6:10684924:C:CC	acceptor_gain	0.9700
6:10671596:GAT:G	acceptor_gain	0.9600
6:10683229:TTTCC:T	acceptor_loss	0.9600
6:10683230:TTCCT:T	acceptor_loss	0.9600
6:10683233:C:A	acceptor_loss	0.9600
6:10683234:TG:T	acceptor_loss	0.9600
6:10683235:G:C	acceptor_loss	0.9600
6:10683239:CAAAA:C	acceptor_loss	0.9600
6:10684931:C:CT	acceptor_gain	0.9600
6:10671595:GGAT:G	acceptor_gain	0.9500
6:10671618:A:C	acceptor_gain	0.9400
6:10683181:TGTTA:T	donor_loss	0.9400
6:10683183:TTA:T	donor_loss	0.9400

AlphaMissense

1014 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:10671507:C:A	W136C	0.990
6:10671507:C:G	W136C	0.990
6:10671543:A:C	S124R	0.987
6:10671543:A:T	S124R	0.987
6:10671545:T:G	S124R	0.987
6:10671509:A:G	W136R	0.986
6:10671509:A:T	W136R	0.986
6:10671523:A:G	L131P	0.975
6:10671527:A:G	S130P	0.972
6:10671555:A:C	F120L	0.964
6:10671555:A:T	F120L	0.964
6:10671556:A:G	F120S	0.964
6:10671557:A:G	F120L	0.964
6:10671508:C:G	W136S	0.962
6:10671535:A:G	L127P	0.961
6:10671523:A:T	L131H	0.956
6:10671508:C:A	W136L	0.950
6:10671544:C:A	S124I	0.949
6:10671509:A:C	W136G	0.929
6:10671515:A:G	C134R	0.929
6:10671556:A:C	F120C	0.920
6:10671513:G:C	C134W	0.919
6:10671478:A:G	I146T	0.917
6:10671523:A:C	L131R	0.906
6:10671564:G:C	N117K	0.902
6:10671564:G:T	N117K	0.902
6:10671496:T:A	D140V	0.901
6:10671497:C:G	D140H	0.899
6:10671544:C:T	S124N	0.898
6:10671541:T:A	E125V	0.893

dbSNP variants (sampled 300 via entrez): RS1000038898 (6:10694166 AG>A), RS1000236696 (6:10684016 GA>G), RS1000252202 (6:10676941 G>A), RS1000403623 (6:10675516 C>A,T), RS1000459014 (6:10688858 C>A,T), RS1000524099 (6:10679630 A>G), RS1000556617 (6:10679983 T>C), RS1000763656 (6:10687299 G>A,T), RS1000828050 (6:10688572 T>C), RS1000972574 (6:10685823 G>C), RS1001034243 (6:10678830 C>T), RS1001319000 (6:10680762 G>A,C), RS1001463349 (6:10695389 A>G), RS1001470653 (6:10674773 T>A), RS1001490726 (6:10677865 T>C)

Disease associations

OMIM: gene MIM:621281 | disease phenotypes: MIM:116700

GenCC curated gene-disease

Mondo (1): cataract 13 with adult I phenotype (MONDO:0007289)

Orphanet (1): Early onset non-syndromic cataract (Orphanet:91492)

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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases methylation, increases expression	4
aristolochic acid I	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Vorinostat	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	decreases expression, increases abundance	1
Formaldehyde	increases expression	1
Indomethacin	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	affects expression	1
Aflatoxin B1	increases expression	1
Cadmium Chloride	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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