CXorf58

Summary

CXorf58 (chromosome X open reading frame 58, HGNC:26356) is a protein-coding gene on chromosome Xp22.11, encoding Uncharacterized protein CXorf58 (Q96LI9).

At a glance

• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_152761

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26356
Approved symbol	CXorf58
Name	chromosome X open reading frame 58
Location	Xp22.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25444
Ensembl gene	ENSG00000165182
Ensembl biotype	protein_coding
Entrez	254158

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000379211, ENST00000435707, ENST00000648352, ENST00000899642

RefSeq mRNA: 2 — MANE Select: NM_152761 NM_001169574, NM_152761

CCDS: CCDS14209

Canonical transcript exons

ENST00000379211 — 9 exons

Exon	Start	End
ENSE00001091044	23938547	23938700
ENSE00001091045	23935196	23935425
ENSE00001091048	23927239	23927370
ENSE00001091049	23911757	23911856
ENSE00001091051	23916217	23916328
ENSE00001091052	23915700	23915794
ENSE00001480110	23910283	23910418
ENSE00001480111	23908006	23908329
ENSE00003834186	23939244	23939509

Expression profiles

Bgee: expression breadth broad, 90 present calls, max score 85.82.

Top tissues by expression

195 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	85.82	gold quality
sperm	CL:0000019	77.35	gold quality
buccal mucosa cell	CL:0002336	74.49	silver quality
testis	UBERON:0000473	61.76	gold quality
left testis	UBERON:0004533	61.76	gold quality
right testis	UBERON:0004534	61.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	57.71	gold quality
hindlimb stylopod muscle	UBERON:0004252	56.97	gold quality
islet of Langerhans	UBERON:0000006	55.98	gold quality
bronchial epithelial cell	CL:0002328	55.66	silver quality
bronchus	UBERON:0002185	54.95	silver quality
right uterine tube	UBERON:0001302	52.99	gold quality
oviduct epithelium	UBERON:0004804	51.90	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	51.79	gold quality
nasal cavity mucosa	UBERON:0001826	48.86	gold quality
pancreas	UBERON:0001264	47.04	gold quality
fallopian tube	UBERON:0003889	46.98	gold quality
right adrenal gland cortex	UBERON:0035827	46.56	gold quality
right adrenal gland	UBERON:0001233	46.46	gold quality
left adrenal gland	UBERON:0001234	46.38	gold quality
adrenal gland	UBERON:0002369	45.47	gold quality
heart left ventricle	UBERON:0002084	45.04	gold quality
cardiac ventricle	UBERON:0002082	44.87	gold quality
adrenal tissue	UBERON:0018303	44.76	silver quality
skeletal muscle tissue	UBERON:0001134	44.67	silver quality
lower esophagus mucosa	UBERON:0035834	44.60	silver quality
adrenal cortex	UBERON:0001235	44.16	gold quality
left adrenal gland cortex	UBERON:0035825	43.93	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
muscle tissue	UBERON:0002385	43.34	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CXorf58, 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-4534	99.99	66.58	1907
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-6853-3P	99.36	70.79	1558
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-1911-3P	99.15	66.17	528
HSA-MIR-1226-3P	97.51	66.32	1063
HSA-MIR-4445-5P	97.21	66.16	832
HSA-MIR-6730-3P	97.03	67.54	889
HSA-MIR-301A-5P	96.88	68.07	931
HSA-MIR-301B-5P	96.88	67.75	946
HSA-MIR-6753-5P	94.70	64.08	470

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fam90a1b	ENSMUSG00000118554
rattus_norvegicus	Cxhxorf58	ENSRNOG00000051365

Protein

Protein identifiers

Uncharacterized protein CXorf58 — Q96LI9 (reviewed: Q96LI9)

All UniProt accessions (3): A0A3B3ISQ8, H7C2Q7, Q96LI9

RefSeq proteins (2): NP_001163045, NP_689974* (*=MANE)

Domains & families (InterPro)

UniProt features (4 total): sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LI9-F1	76.34	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 40 (showing top): CAGCTG_AP4_Q5, TGIF_01, CYTAGCAAY_UNKNOWN, RFX1_01, DODD_NASOPHARYNGEAL_CARCINOMA_DN, VDR_Q6, chrXp22, PEDRIOLI_MIR31_TARGETS_UP, H1_6_TARGET_GENES, ZBTB12_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF10_TARGET_GENES, ZNF329_TARGET_GENES, ZNF407_TARGET_GENES, ZNF597_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

158 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CXorf58	C19orf81	C9J6K1	771
CXorf58	SMLR1	H3BR10	770
CXorf58	AXDND1	Q5T1B0	694
CXorf58	C7orf25	Q9BPX7	666
CXorf58	RSRP1	Q9BUV0	607
CXorf58	CIMIP1	Q9H1P6	582
CXorf58	CFAP46	Q8IYW2	573
CXorf58	ZBTB21	Q9ULJ3	512
CXorf58	SPR	P35270	473
CXorf58	TEX261	Q6UWH6	445
CXorf58	SLC25A52	Q3SY17	419
CXorf58	ATAD3C	Q5T2N8	355
CXorf58	RASGEF1A	Q8N9B8	311
CXorf58	SLC25A51	Q9H1U9	305
CXorf58	RGS1	Q08116	301

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CXorf58	GDE1	psi-mi:“MI:0915”(physical association)	0.560
CXorf58	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
CXorf58	DCAF5	psi-mi:“MI:0915”(physical association)	0.400
CXorf58	TGFBR2	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): GDE1 (Affinity Capture-MS), GDE1 (Affinity Capture-MS), CXorf58 (Synthetic Lethality), CXorf58 (Proximity Label-MS), HOXA1 (Affinity Capture-MS), GDE1 (Affinity Capture-MS), TGFBR2 (Affinity Capture-MS), DCAF5 (Affinity Capture-MS)

ESM2 similar proteins: A0A571BF63, A0A5F8MPE6, A1A535, A8QHQ0, B0W730, O23463, O46470, O54829, O64851, O82645, P49758, P49802, P49803, P49809, Q058N0, Q0VA04, Q14D04, Q28IH8, Q4R6I5, Q4R7Z7, Q502W7, Q569B9, Q5PQS3, Q5SPP5, Q5XG48, Q5XIR8, Q641A2, Q6ZQ18, Q7T0S7, Q86VD1, Q8BG67, Q8BMD7, Q8CDN8, Q8H1E8, Q8IGJ0, Q8N957, Q8NCR3, Q8NHS4, Q96L03, Q96LI9

Diamond homologs: A0A5F8MPE6, Q96LI9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1537 predictions. Top by Δscore:

Variant	Effect	Δscore
X:23910277:TTTCA:T	acceptor_loss	1.0000
X:23910278:TTCA:T	acceptor_loss	1.0000
X:23910281:A:T	acceptor_loss	1.0000
X:23910414:CTATC:C	donor_gain	1.0000
X:23910419:G:GG	donor_gain	1.0000
X:23916283:TTAC:T	donor_gain	1.0000
X:23916324:G:GG	donor_gain	1.0000
X:23927235:A:AG	acceptor_gain	1.0000
X:23927237:A:AG	acceptor_gain	1.0000
X:23927237:A:G	acceptor_loss	1.0000
X:23927237:AG:A	acceptor_gain	1.0000
X:23927238:G:GA	acceptor_gain	1.0000
X:23927238:GG:G	acceptor_gain	1.0000
X:23927238:GGC:G	acceptor_gain	1.0000
X:23927238:GGCA:G	acceptor_gain	1.0000
X:23927320:TCCA:T	donor_gain	1.0000
X:23927326:G:GG	donor_gain	1.0000
X:23927371:G:GG	donor_gain	1.0000
X:23935403:C:G	donor_gain	1.0000
X:23907951:G:GT	donor_gain	0.9900
X:23908182:G:GT	donor_gain	0.9900
X:23908233:G:GT	donor_gain	0.9900
X:23910281:A:AG	acceptor_gain	0.9900
X:23910282:G:GG	acceptor_gain	0.9900
X:23910282:GATT:G	acceptor_gain	0.9900
X:23910415:TATCG:T	donor_loss	0.9900
X:23910416:ATC:A	donor_gain	0.9900
X:23910416:ATCGT:A	donor_loss	0.9900
X:23910417:TC:T	donor_gain	0.9900
X:23910417:TCG:T	donor_loss	0.9900

AlphaMissense

2193 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:23935250:T:A	W204R	0.994
X:23935250:T:C	W204R	0.994
X:23916233:T:C	F110L	0.992
X:23916235:T:A	F110L	0.992
X:23916235:T:G	F110L	0.992
X:23935254:G:C	R205P	0.991
X:23915791:T:C	F103S	0.990
X:23916251:T:C	F116L	0.989
X:23916253:T:A	F116L	0.989
X:23916253:T:G	F116L	0.989
X:23916255:A:T	K117I	0.988
X:23911824:T:C	F62L	0.987
X:23911826:T:A	F62L	0.987
X:23911826:T:G	F62L	0.987
X:23935253:C:A	R205S	0.987
X:23916219:T:C	F105S	0.986
X:23935252:G:C	W204C	0.986
X:23935252:G:T	W204C	0.986
X:23916256:A:C	K117N	0.982
X:23916256:A:T	K117N	0.982
X:23911831:T:C	L64P	0.980
X:23935260:T:C	L207S	0.979
X:23911834:T:C	L65P	0.978
X:23935299:A:T	D220V	0.977
X:23915748:G:C	A89P	0.976
X:23935246:C:A	N202K	0.974
X:23935246:C:G	N202K	0.974
X:23935299:A:C	D220A	0.974
X:23916240:C:A	P112H	0.973
X:23916254:A:G	K117E	0.972

dbSNP variants (sampled 300 via entrez): RS1000277974 (X:23911588 AT>A), RS1000394046 (X:23929924 G>A), RS1000451000 (X:23912465 C>T), RS1000880066 (X:23908802 A>G), RS1000929118 (X:23912125 G>A), RS1000985429 (X:23921440 T>C), RS1001039253 (X:23921038 A>T), RS1001128296 (X:23937376 T>C), RS1001463195 (X:23911465 A>G), RS1001904584 (X:23920385 A>G), RS1002090229 (X:23911222 T>A,C), RS1002240171 (X:23920781 C>T), RS1002252459 (X:23920319 G>A), RS1002308636 (X:23929837 A>G), RS1002455439 (X:23907402 G>A)

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

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment, affects response to substance	1
abrine	increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Carbamazepine	affects expression	1
Lipopolysaccharides	affects cotreatment, affects response to substance, increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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