CXorf38

Summary

CXorf38 (chromosome X open reading frame 38, HGNC:28589) is a protein-coding gene on chromosome Xp11.4, encoding Uncharacterized protein CXorf38 (Q8TB03).

Located in mitochondrion.

Source: NCBI Gene 159013 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_144970

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28589
Approved symbol	CXorf38
Name	chromosome X open reading frame 38
Location	Xp11.4
Locus type	gene with protein product
Status	Approved
Aliases	MGC39350
Ensembl gene	ENSG00000185753
Ensembl biotype	protein_coding
OMIM	301117
Entrez	159013

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 15 protein_coding

ENST00000327877, ENST00000378421, ENST00000378426, ENST00000897030, ENST00000897031, ENST00000897032, ENST00000971736, ENST00000971737, ENST00000971738, ENST00000971739, ENST00000971740, ENST00000971741, ENST00000971742, ENST00000971743, ENST00000971744

RefSeq mRNA: 2 — MANE Select: NM_144970 NM_001330455, NM_144970

CCDS: CCDS14253, CCDS83467

Canonical transcript exons

ENST00000327877 — 7 exons

Exon	Start	End
ENSE00001307502	40636533	40636712
ENSE00001309111	40639009	40639128
ENSE00001325327	40630614	40630773
ENSE00001330904	40637007	40637156
ENSE00001886287	40626921	40630162
ENSE00001958051	40647305	40647561
ENSE00003568400	40647007	40647141

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 91.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.8959 / max 125.4200, expressed in 1809 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198946	14.4729	1809
198945	0.4230	164

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	91.28	gold quality
leukocyte	CL:0000738	91.08	gold quality
epithelial cell of pancreas	CL:0000083	90.64	gold quality
oviduct epithelium	UBERON:0004804	90.60	gold quality
granulocyte	CL:0000094	88.46	gold quality
blood	UBERON:0000178	88.46	gold quality
palpebral conjunctiva	UBERON:0001812	88.14	gold quality
secondary oocyte	CL:0000655	86.74	gold quality
amniotic fluid	UBERON:0000173	86.67	gold quality
oocyte	CL:0000023	85.42	gold quality
pancreatic ductal cell	CL:0002079	84.58	gold quality
lymph node	UBERON:0000029	84.45	gold quality
buccal mucosa cell	CL:0002336	83.83	gold quality
thymus	UBERON:0002370	83.58	gold quality
fallopian tube	UBERON:0003889	83.01	gold quality
epithelium of nasopharynx	UBERON:0001951	82.59	gold quality
spleen	UBERON:0002106	82.47	gold quality
jejunal mucosa	UBERON:0000399	82.09	gold quality
vermiform appendix	UBERON:0001154	81.93	gold quality
endometrium	UBERON:0001295	81.59	gold quality
bone marrow	UBERON:0002371	81.22	gold quality
caecum	UBERON:0001153	80.86	gold quality
germinal epithelium of ovary	UBERON:0001304	80.81	gold quality
bone marrow cell	CL:0002092	80.42	gold quality
tonsil	UBERON:0002372	80.09	gold quality
thyroid gland	UBERON:0002046	79.96	gold quality
right lobe of thyroid gland	UBERON:0001119	79.77	gold quality
left lobe of thyroid gland	UBERON:0001120	79.77	gold quality
islet of Langerhans	UBERON:0000006	79.35	gold quality
right adrenal gland cortex	UBERON:0035827	79.28	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

93 targeting CXorf38, 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-3163	100.00	77.23	8605
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-548U	99.65	67.78	1463

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-91p5.3	ENSDARG00000089227
mus_musculus	1810030O07Rik	ENSMUSG00000044148
rattus_norvegicus	Cxhxorf38	ENSRNOG00000023187

Protein

Protein identifiers

Uncharacterized protein CXorf38 — Q8TB03 (reviewed: Q8TB03)

All UniProt accessions (1): Q8TB03

Isoforms (3)

UniProt ID	Names	Canonical?
Q8TB03-1	1	yes
Q8TB03-2	2
Q8TB03-3	3

RefSeq proteins (2): NP_001317384, NP_659407* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027897	DUF4559	Family

Pfam: PF15112

UniProt features (7 total): splice variant 3, modified residue 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TB03-F1	87.43	0.67

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): 61, 314

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP, ACEVEDO_LIVER_CANCER_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, chrXp11, RAO_BOUND_BY_SALL4_ISOFORM_B, GCNP_SHH_UP_EARLY.V1_UP, NPAT_TARGET_GENES, SETD7_TARGET_GENES, ZNF664_TARGET_GENES, MIR4795_3P, MIR3121_3P, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP

GO Biological Process (0):

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

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2096 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CXorf38	ZNF182	P17025	491
CXorf38	EIF2S3	P41091	444
CXorf38	LIPT1	Q9Y234	432
CXorf38	ABRACL	Q9P1F3	430
CXorf38	TMEM164	Q5U3C3	422
CXorf38	TCEANC	Q8N8B7	419
CXorf38	TLL2	Q9Y6L7	419
CXorf38	DENND10	Q8TCE6	412
CXorf38	C11orf71	Q6IPW1	404
CXorf38	ZNF524	Q96C55	397
CXorf38	RIBC1	Q8N443	381
CXorf38	MTMR1	Q13613	380
CXorf38	C1orf174	Q8IYL3	370
CXorf38	CSTPP1	Q9H6J7	367
CXorf38	ARL16	Q0P5N6	366

IntAct

66 interactions, top by confidence:

A	B	Type	Score
PAX6	CXorf38	psi-mi:“MI:0915”(physical association)	0.560
NFYC	CXorf38	psi-mi:“MI:0915”(physical association)	0.560
CDHR3	CXorf38	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	CXorf38	psi-mi:“MI:0915”(physical association)	0.560
PAX5	CXorf38	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	DMWD	psi-mi:“MI:0915”(physical association)	0.560
CXorf38		psi-mi:“MI:0915”(physical association)	0.560
CXorf38	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	GRN	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	TSC1	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	WFS1	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	KIF1B	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	RNF11	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
CXorf38	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
HTT	CXorf38	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (10): CXorf38 (Two-hybrid), CXorf38 (Two-hybrid), CXorf38 (Two-hybrid), CXorf38 (Two-hybrid), PAX5 (Two-hybrid), CXorf38 (Affinity Capture-MS), POTEF (Affinity Capture-MS), CXorf38 (Affinity Capture-MS), CXorf38 (Positive Genetic), CXorf38 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2RT67, A4IFQ0, B0CM32, B0KW86, O60443, O95456, Q0P5F2, Q13769, Q14159, Q1A730, Q1JQA1, Q1RMS8, Q1RMZ1, Q29108, Q2KHT6, Q3B7L5, Q3T0J1, Q3ZK22, Q4R372, Q5E9K8, Q5FVM3, Q5M7Q1, Q5RFG8, Q5RFL7, Q5XI52, Q5ZJ87, Q62522, Q641X7, Q68FX7, Q76JQ2, Q7Z6J8, Q8BXK4, Q8C5K5, Q8CHQ0, Q8IWR0, Q8K2I9, Q8NFZ0, Q8QZS3, Q8TB03, Q8TCJ0

Diamond homologs: Q8C5K5, Q8TB03

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

775 predictions. Top by Δscore:

Variant	Effect	Δscore
X:40630769:GAGAG:G	acceptor_gain	1.0000
X:40630770:AGAG:A	acceptor_gain	1.0000
X:40630771:GAG:G	acceptor_gain	1.0000
X:40630771:GAGCT:G	acceptor_loss	1.0000
X:40630772:AG:A	acceptor_gain	1.0000
X:40630773:GCT:G	acceptor_loss	1.0000
X:40630774:C:CC	acceptor_gain	1.0000
X:40630774:CTGCA:C	acceptor_loss	1.0000
X:40630775:T:A	acceptor_loss	1.0000
X:40637001:TTTTA:T	donor_loss	1.0000
X:40637002:TTTAC:T	donor_loss	1.0000
X:40637003:TTACC:T	donor_loss	1.0000
X:40637004:TAC:T	donor_loss	1.0000
X:40637005:A:C	donor_loss	1.0000
X:40637006:C:CA	donor_loss	1.0000
X:40637152:ATTAC:A	acceptor_gain	1.0000
X:40637153:TTAC:T	acceptor_gain	1.0000
X:40637154:TAC:T	acceptor_gain	1.0000
X:40637154:TACC:T	acceptor_loss	1.0000
X:40637155:AC:A	acceptor_gain	1.0000
X:40637155:ACCTG:A	acceptor_loss	1.0000
X:40637156:CC:C	acceptor_gain	1.0000
X:40637157:C:CC	acceptor_gain	1.0000
X:40637157:CT:C	acceptor_loss	1.0000
X:40637160:C:CT	acceptor_gain	1.0000
X:40637161:A:T	acceptor_gain	1.0000
X:40639003:TCTTA:T	donor_loss	1.0000
X:40639004:CTTAC:C	donor_loss	1.0000
X:40639005:TTACC:T	donor_loss	1.0000
X:40639006:TACC:T	donor_loss	1.0000

AlphaMissense

2093 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:40647036:A:G	W108R	0.996
X:40647036:A:T	W108R	0.996
X:40647058:C:A	W100C	0.996
X:40647058:C:G	W100C	0.996
X:40647060:A:G	W100R	0.996
X:40647060:A:T	W100R	0.996
X:40647111:A:G	W83R	0.996
X:40647111:A:T	W83R	0.996
X:40647034:C:A	W108C	0.995
X:40647034:C:G	W108C	0.995
X:40647021:A:G	W113R	0.992
X:40647021:A:T	W113R	0.992
X:40647007:C:A	K117N	0.991
X:40647007:C:G	K117N	0.991
X:40647469:A:G	W18R	0.991
X:40647469:A:T	W18R	0.991
X:40647052:G:C	N102K	0.990
X:40647052:G:T	N102K	0.990
X:40647109:C:A	W83C	0.990
X:40647109:C:G	W83C	0.990
X:40637144:G:T	R162S	0.989
X:40639123:G:C	F119L	0.989
X:40639123:G:T	F119L	0.989
X:40639125:A:G	F119L	0.989
X:40637143:C:G	R162P	0.988
X:40647011:G:T	A116D	0.986
X:40647019:C:A	W113C	0.986
X:40647019:C:G	W113C	0.986
X:40647059:C:G	W100S	0.984
X:40647467:C:A	W18C	0.984

dbSNP variants (sampled 300 via entrez): RS1000755724 (X:40640813 G>A), RS1001147065 (X:40640246 T>A), RS1001585051 (X:40639836 C>G,T), RS1001638601 (X:40627903 G>T), RS1001684998 (X:40634984 G>A), RS1001712097 (X:40646300 C>G), RS1001784184 (X:40645583 C>G), RS1002119770 (X:40647629 C>T), RS1002392091 (X:40630003 T>C), RS1002699618 (X:40645103 G>A), RS1002711114 (X:40645619 T>C), RS1003095905 (X:40633100 C>T), RS1003126594 (X:40627625 G>C), RS1003245064 (X:40636154 C>G,T), RS1003431348 (X:40627896 C>T)

Disease associations

OMIM: gene MIM:301117 | 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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
sodium arsenite	decreases expression, increases expression	2
Nickel	increases expression	2
Valproic Acid	decreases expression	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
zinc chromate	increases abundance, increases expression	1
potassium chromate(VI)	decreases expression	1
nickel sulfate	decreases expression	1
coumarin	increases phosphorylation	1
resorcinol	decreases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	increases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Dexamethasone	decreases expression, affects cotreatment	1
Indomethacin	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Thimerosal	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Vanadates	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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