CXorf66

Summary

CXorf66 (chromosome X open reading frame 66, HGNC:33743) is a protein-coding gene on chromosome Xq27.1, encoding Uncharacterized protein CXorf66 (Q5JRM2).

The protein encoded by this gene is predicted to be a type I membrane protein, however, its exact function is not known.

Source: NCBI Gene 347487 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_001013403

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33743
Approved symbol	CXorf66
Name	chromosome X open reading frame 66
Location	Xq27.1
Locus type	gene with protein product
Status	Approved
Aliases	RP11-35F15.2, SGPX
Ensembl gene	ENSG00000203933
Ensembl biotype	protein_coding
Entrez	347487

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000370540

RefSeq mRNA: 1 — MANE Select: NM_001013403 NM_001013403

CCDS: CCDS35411

Canonical transcript exons

ENST00000370540 — 3 exons

Exon	Start	End
ENSE00001452973	139955728	139956739
ENSE00001452974	139958064	139958217
ENSE00001452975	139965409	139965521

Expression profiles

Bgee: expression breadth broad, 12 present calls, max score 83.32.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0133 / max 10.0930, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200723	0.0133	4

Top tissues by expression

123 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	83.32	gold quality
cerebellar vermis	UBERON:0004720	82.71	gold quality
left testis	UBERON:0004533	80.07	gold quality
testis	UBERON:0000473	79.97	gold quality
right testis	UBERON:0004534	79.70	gold quality
quadriceps femoris	UBERON:0001377	69.42	gold quality
thymus	UBERON:0002370	61.19	silver quality
liver	UBERON:0002107	42.23	gold quality
right lobe of liver	UBERON:0001114	37.32	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	35.20	gold quality
muscle tissue	UBERON:0002385	32.41	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.89	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
uterine cervix	UBERON:0000002	27.38	gold quality
tonsil	UBERON:0002372	27.05	gold quality
urinary bladder	UBERON:0001255	26.74	gold quality
blood	UBERON:0000178	26.71	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
metanephros cortex	UBERON:0010533	26.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CXorf66, 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-8062	99.88	68.43	995
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-216B-3P	98.55	67.19	1223
HSA-MIR-6757-5P	98.08	65.50	724
HSA-MIR-4715-5P	97.62	67.47	506
HSA-MIR-6892-5P	97.27	68.60	847
HSA-MIR-4259	95.68	65.25	582
HSA-MIR-1281	92.96	65.73	260

Literature-anchored findings (GeneRIF, showing 1)

• The SGPX gene is a putative novel cancer biomarker. [Meta-analysis] (PMID:24709545)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm7073	ENSMUSG00000079583
rattus_norvegicus	Cxhxorf66	ENSRNOG00000037399

Protein

Protein identifiers

Uncharacterized protein CXorf66 — Q5JRM2 (reviewed: Q5JRM2)

All UniProt accessions (1): Q5JRM2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001013421* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038873	CXorf66	Family

UniProt features (14 total): compositionally biased region 4, region of interest 3, topological domain 2, signal peptide 1, chain 1, glycosylation site 1, sequence variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JRM2-F1	54.03	0.02

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chrXq27, ZNF362_TARGET_GENES, MIR1290, MIR3145_3P, MIR1281

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

3707 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CXorf66	DIPK2B	Q9H7Y0	506
CXorf66	HIGD1C	A8MV81	480
CXorf66	COQ5	Q5HYK3	358
CXorf66	ATP11C	Q8NB49	351
CXorf66	FAU	P35544	350
CXorf66	YARS1	P54577	350
CXorf66	RPS3	P23396	349
CXorf66	RPLP1	P05386	348
CXorf66	RPS3A	P33443	348
CXorf66	RPL5	P46777	348
CXorf66	RPLP0	P05388	348
CXorf66	RPS28	P25112	348
CXorf66	EIF3G	O75821	347
CXorf66	RPS26	P02383	347
CXorf66	RPL30	P04645	347
CXorf66	VARS1	P26640	347

IntAct

39 interactions, top by confidence:

A	B	Type	Score
EMD	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
LAT	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
RTP2	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
ASPH	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	RPRM	psi-mi:“MI:0915”(physical association)	0.560
AQP6	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	TMX2	psi-mi:“MI:0915”(physical association)	0.560
STX10	CXorf66	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	POMGNT1	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	RTP2	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	YIPF6	psi-mi:“MI:0915”(physical association)	0.560
CXorf66	PRUNE1	psi-mi:“MI:0915”(physical association)	0.500
CXorf66	LRP4	psi-mi:“MI:0914”(association)	0.350
CXorf66		psi-mi:“MI:0915”(physical association)	0.000
CXorf66	AQP6	psi-mi:“MI:0915”(physical association)	0.000
CXorf66	TMX2	psi-mi:“MI:0915”(physical association)	0.000
STX10	CXorf66	psi-mi:“MI:0915”(physical association)	0.000
POMGNT1	CXorf66	psi-mi:“MI:0915”(physical association)	0.000
CXorf66	ERGIC3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (35): CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), CXorf66 (Two-hybrid), TMX2 (Two-hybrid), LAT (Two-hybrid), DSG4 (Affinity Capture-MS), TRIM29 (Affinity Capture-MS), ANKRD50 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GR13, A2AEY4, B0QZF7, B3SRR7, B3SRX3, H2KZ49, O13757, O49498, O74981, P04515, P17467, P18036, P18037, P19715, P23047, P34338, P34627, P35662, P35663, P40167, P46013, P52529, P52530, P70486, Q01030, Q03703, Q04003, Q06813, Q09280, Q09458, Q11114, Q12418, Q2YDJ5, Q32LB6, Q3ZK65, Q4QY64, Q4V7B4, Q5JRM2, Q5M948, Q5RCX3

Diamond homologs: Q2YDJ5, Q5JRM2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

421 predictions. Top by Δscore:

Variant	Effect	Δscore
X:139965406:TAC:T	donor_loss	1.0000
X:139965407:A:AC	donor_gain	0.9900
X:139965408:C:CC	donor_gain	0.9900
X:139958062:A:AC	donor_gain	0.9800
X:139958063:C:CC	donor_gain	0.9800
X:139958062:ACATT:A	donor_gain	0.9700
X:139958063:CATTC:C	donor_gain	0.9700
X:139959714:T:TA	donor_gain	0.9700
X:139956738:CC:C	acceptor_gain	0.9600
X:139956739:CC:C	acceptor_gain	0.9600
X:139965405:CTACC:C	donor_gain	0.9600
X:139965406:TACCT:T	donor_gain	0.9600
X:139958063:CATT:C	donor_gain	0.9500
X:139958151:A:AC	donor_gain	0.9500
X:139958152:C:CC	donor_gain	0.9500
X:139958144:A:AC	donor_gain	0.9300
X:139965407:AC:A	donor_gain	0.9300
X:139965408:CC:C	donor_gain	0.9300
X:139956737:ACCC:A	acceptor_loss	0.9200
X:139956738:CCCTG:C	acceptor_loss	0.9200
X:139956739:CCTGA:C	acceptor_loss	0.9200
X:139956741:T:G	acceptor_loss	0.9200
X:139958056:AAACT:A	donor_loss	0.9000
X:139958057:AACTT:A	donor_loss	0.9000
X:139958058:ACTT:A	donor_loss	0.9000
X:139958059:CT:C	donor_loss	0.9000
X:139958060:TTA:T	donor_loss	0.9000
X:139958061:T:TC	donor_loss	0.9000
X:139958062:A:C	donor_loss	0.9000
X:139958063:C:CA	donor_loss	0.9000

AlphaMissense

2356 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:139958149:C:G	G53R	0.907
X:139958119:A:G	C63R	0.857
X:139958148:C:T	G53D	0.797
X:139958129:A:C	F59L	0.770
X:139958129:A:T	F59L	0.770
X:139958131:A:G	F59L	0.770
X:139958171:T:A	R45S	0.744
X:139958171:T:G	R45S	0.744
X:139965460:A:G	W13R	0.742
X:139965460:A:T	W13R	0.742
X:139965481:A:G	C6R	0.742
X:139958136:A:C	M57R	0.721
X:139956052:A:C	F310L	0.720
X:139956052:A:T	F310L	0.720
X:139956054:A:G	F310L	0.720
X:139965477:A:T	V7D	0.715
X:139965474:A:C	L8R	0.696
X:139958114:A:C	F64L	0.693
X:139958114:A:T	F64L	0.693
X:139958116:A:G	F64L	0.693
X:139958136:A:T	M57K	0.690
X:139958113:A:G	C65R	0.658
X:139965458:C:A	W13C	0.649
X:139965458:C:G	W13C	0.649
X:139956244:T:A	K246N	0.642
X:139956244:T:G	K246N	0.642
X:139965471:A:C	L9R	0.642
X:139958106:A:G	L67P	0.634
X:139958163:A:G	L48P	0.632
X:139958117:A:C	C63W	0.620

dbSNP variants (sampled 300 via entrez): RS1000204301 (X:139958382 T>C), RS1000216228 (X:139967314 G>A), RS1000297835 (X:139964307 A>G), RS1000400541 (X:139957029 G>A), RS1000478437 (X:139966641 A>AAATT), RS1000501603 (X:139962735 G>A), RS1000635460 (X:139962408 T>A), RS1000730434 (X:139956180 G>A,T), RS1001232417 (X:139955669 G>A,C,T), RS1001263467 (X:139956062 G>A), RS1001478672 (X:139963795 A>G), RS1001569171 (X:139965166 A>G), RS1001846038 (X:139963431 A>G), RS1002115488 (X:139955530 T>C), RS1002651791 (X:139962841 A>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)

Clinical trials (associated diseases)

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