CPXCR1

Summary

CPXCR1 (CPX chromosome region candidate 1, HGNC:2332) is a protein-coding gene on chromosome Xq21.31, encoding CPX chromosomal region candidate gene 1 protein (Q8N123).

This gene is one of several genes identified in a region of the X chromosome associated with an X-linked cleft palate (CPX) disorder. The encoded protein contains a motif similar to a motif found in zinc-finger proteins. Mutation analysis of this gene has not revealed any mutation which causes the CPX disorder. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 53336 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 58 total — 1 pathogenic
• MANE Select transcript: NM_033048

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2332
Approved symbol	CPXCR1
Name	CPX chromosome region candidate 1
Location	Xq21.31
Locus type	gene with protein product
Status	Approved
Aliases	CT77
Ensembl gene	ENSG00000147183
Ensembl biotype	protein_coding
OMIM	301055
Entrez	53336

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000276127, ENST00000373111, ENST00000614120

RefSeq mRNA: 2 — MANE Select: NM_033048 NM_001184771, NM_033048

CCDS: CCDS14458

Canonical transcript exons

ENST00000276127 — 3 exons

Exon	Start	End
ENSE00001209592	88749318	88749423
ENSE00001280810	88747225	88747369
ENSE00003889331	88753407	88754781

Expression profiles

Bgee: expression breadth broad, 16 present calls, max score 83.22.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	83.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.12	gold quality
left testis	UBERON:0004533	64.80	gold quality
testis	UBERON:0000473	64.23	gold quality
right testis	UBERON:0004534	63.77	gold quality
secondary oocyte	CL:0000655	63.40	gold quality
lower lobe of lung	UBERON:0008949	52.22	silver quality
adult organism	UBERON:0007023	47.48	silver quality
oocyte	CL:0000023	44.42	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
oviduct epithelium	UBERON:0004804	42.50	gold quality
upper leg skin	UBERON:0004262	41.67	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
subthalamic nucleus	UBERON:0001906	40.80	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
dorsal plus ventral thalamus	UBERON:0001897	40.11	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting CPXCR1, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-4320	99.75	65.80	793
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-550A-3P	98.37	69.61	632
HSA-MIR-4469	97.93	65.81	1319

Literature-anchored findings (GeneRIF, showing 1)

• Our results indicate a possible contribution of CNVs in LEPR, NEGR1, ARHGEF4, and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d to the development of obesity, particularly abdominal obesity in Mexican children. (PMID:28428959)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cpxcr1	ENSMUSG00000072995

Protein

Protein identifiers

CPX chromosomal region candidate gene 1 protein — Q8N123 (reviewed: Q8N123)

Alternative names: Cancer/testis antigen 77

All UniProt accessions (1): Q8N123

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in a variety of fetal tissues.

RefSeq proteins (2): NP_001171700, NP_149037* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain

UniProt features (5 total): sequence variant 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N123-F1	49.90	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): CYTAGCAAY_UNKNOWN, RFX1_01, chrXq21, NFE2L2.V2, MIR548E_5P, MIR3942_3P, MIR3145_3P, MIR8084, MIR550A_3P, MIR200C_5P, MIR4320, GSE11973_MIR223_KOVS_WT_BONE_MARROW_NEUTROPHIL_DN, MYOCD_TARGET_GENES, ZNF320_TARGET_GENES, PULVER_FOREY_PERTURB_ACCUMULATION_G1_S

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPXCR1	KLHL4	Q9C0H6	695
CPXCR1	CT62	P0C5K7	610
CPXCR1	SATL1	Q86VE3	583
CPXCR1	CYLC1	P35663	577
CPXCR1	FAM24A	A6NFZ4	572
CPXCR1	TGIF2LX	Q8IUE1	571
CPXCR1	RBM46	Q8TBY0	571
CPXCR1	OR10H5	Q8NGA6	507
CPXCR1	MAGEB2	O15479	492
CPXCR1	IQCF6	A8MYZ5	490
CPXCR1	PAGE2B	Q5JRK9	485
CPXCR1	PRSS54	Q6PEW0	479
CPXCR1	EPPIN	O95925	479
CPXCR1	CCDC110	Q8TBZ0	476
CPXCR1	ZNF165	P49910	447
CPXCR1	DCAF12L2	Q5VW00	447

IntAct

5 interactions, top by confidence:

A	B	Type	Score
Dlg4	CPXCR1	psi-mi:“MI:0407”(direct interaction)	0.440
CPXCR1	VTA1	psi-mi:“MI:0914”(association)	0.350
CPXCR1	DDI2	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (7): HDGFRP3 (Affinity Capture-MS), VTA1 (Affinity Capture-MS), CHMP3 (Affinity Capture-MS), TUBB2B (Affinity Capture-MS), DDI2 (Affinity Capture-MS), CPXCR1 (Positive Genetic), CPXCR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4J1W7, A0A7H0DN35, A4QN01, A6NHN6, A6NJ64, A8MQ11, E9PIF3, E9PJ23, E9PJI5, E9PKD4, E9PQR5, F5HGC2, F8W1W9, F8WFD2, O75200, O83374, P05913, P06486, P07396, P0C7Q2, P0CK47, P0CK48, P0DM63, P0DXC3, P15489, P16765, P16802, P20969, P36443, P38900, P47003, P68341, P68454, P68455, P87191, P92537, P92561, Q03418, Q32M92, Q4ZGE2

Diamond homologs: Q3V0P1, Q4R6N4, Q8N123

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	44
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
152897	GRCh38/hg38 Xq21.31-22.1(chrX:87807750-100286152)x3	Pathogenic

SpliceAI

191 predictions. Top by Δscore:

Variant	Effect	Δscore
X:88749419:ATTTT:A	donor_gain	1.0000
X:88749420:TTTT:T	donor_gain	1.0000
X:88749424:G:GG	donor_gain	1.0000
X:88747362:GGATC:G	donor_gain	0.9900
X:88747370:G:GG	donor_gain	0.9900
X:88748095:A:AG	donor_gain	0.9900
X:88749312:TTTCA:T	acceptor_loss	0.9900
X:88749313:TTCA:T	acceptor_loss	0.9900
X:88749314:TCA:T	acceptor_loss	0.9900
X:88749315:CA:C	acceptor_loss	0.9900
X:88749316:AG:A	acceptor_gain	0.9900
X:88749317:GG:G	acceptor_gain	0.9900
X:88749317:GGGT:G	acceptor_gain	0.9900
X:88749421:TTT:T	donor_gain	0.9900
X:88749422:TT:T	donor_gain	0.9900
X:88753402:A:G	acceptor_gain	0.9900
X:88753405:A:AG	acceptor_gain	0.9900
X:88753406:G:GG	acceptor_gain	0.9900
X:88747332:G:GG	donor_gain	0.9800
X:88749316:A:AG	acceptor_gain	0.9800
X:88749316:AGG:A	acceptor_gain	0.9800
X:88749316:AGGGT:A	acceptor_gain	0.9800
X:88749317:G:GG	acceptor_gain	0.9800
X:88749317:GGG:G	acceptor_gain	0.9800
X:88749317:GGGTG:G	acceptor_gain	0.9800
X:88749421:TTTGT:T	donor_loss	0.9800
X:88749422:TTG:T	donor_loss	0.9800
X:88749423:TGTG:T	donor_loss	0.9800
X:88749424:G:A	donor_loss	0.9800
X:88749425:T:G	donor_loss	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000252086 (X:88746841 C>G), RS1000558394 (X:88745758 G>A), RS1000589638 (X:88745560 T>C), RS1001153203 (X:88748870 T>C), RS1003119348 (X:88751813 T>C), RS1003310073 (X:88746216 C>T), RS1003539928 (X:88752299 G>A), RS1003572497 (X:88746459 C>A), RS1004398872 (X:88753582 A>G), RS1004431456 (X:88753013 A>G), RS1004693957 (X:88751639 T>C), RS1004725065 (X:88750837 C>T), RS1005144530 (X:88751453 C>A,G), RS1005317634 (X:88753534 G>A,C), RS1005439735 (X:88751775 A>G)

Disease associations

OMIM: gene MIM:301055 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001613_4	Antineutrophil cytoplasmic antibody-associated vasculitis	2.000000e-20

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
testosterone undecanoate	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Levonorgestrel	affects cotreatment, increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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