CPHXL2

Summary

CPHXL2 (cytoplasmic polyadenylated homeobox like 2, HGNC:55919) is a protein-coding gene on chromosome 16q23.1, encoding Cytoplasmic polyadenylated homeobox-like protein 2 (A0A1W2PPK0).

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 112268164 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395862

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:55919
Approved symbol	CPHXL2
Name	cytoplasmic polyadenylated homeobox like 2
Location	16q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000284484
Ensembl biotype	protein_coding
Entrez	112268164

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000640173

RefSeq mRNA: 1 — MANE Select: NM_001395862 NM_001395862

CCDS: CCDS92197

Canonical transcript exons

ENST00000640173 — 3 exons

Exon	Start	End
ENSE00003806701	75660227	75661249
ENSE00003809117	75676987	75677009
ENSE00003810341	75669363	75669556

Expression profiles

Bgee: expression breadth broad, 19 present calls, max score 81.97.

Top tissues by expression

67 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	81.97	gold quality
calcaneal tendon	UBERON:0003701	63.36	gold quality
sural nerve	UBERON:0015488	56.61	silver quality
colonic epithelium	UBERON:0000397	52.69	gold quality
bone marrow cell	CL:0002092	50.03	gold quality
corpus callosum	UBERON:0002336	49.71	silver quality
bone marrow	UBERON:0002371	45.35	gold quality
urinary bladder	UBERON:0001255	44.05	silver quality
skeletal muscle tissue	UBERON:0001134	43.70	gold quality
blood	UBERON:0000178	42.88	silver quality
cortex of kidney	UBERON:0001225	42.06	silver quality
tonsil	UBERON:0002372	41.51	gold quality
ventricular zone	UBERON:0003053	40.99	gold quality
apex of heart	UBERON:0002098	39.58	silver quality
muscle tissue	UBERON:0002385	38.65	gold quality
adrenal tissue	UBERON:0018303	36.75	gold quality
granulocyte	CL:0000094	36.54	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
right lobe of thyroid gland	UBERON:0001119	36.41	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.74	silver quality
primary visual cortex	UBERON:0002436	35.66	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle of leg	UBERON:0001383	35.34	silver quality
descending thoracic aorta	UBERON:0002345	35.22	gold quality
left uterine tube	UBERON:0001303	34.79	silver quality
Brodmann (1909) area 9	UBERON:0013540	34.70	gold quality
monocyte	CL:0000576	34.38	gold quality
leukocyte	CL:0000738	34.32	gold quality
superior frontal gyrus	UBERON:0002661	33.97	gold quality
islet of Langerhans	UBERON:0000006	33.89	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.44

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cphx1	ENSMUSG00000095975
rattus_norvegicus	Cphx1	ENSRNOG00000025433
drosophila_melanogaster	en	FBGN0000577
drosophila_melanogaster	inv	FBGN0001269
caenorhabditis_elegans		WBGENE00000439

Paralogs (3): EN1 (ENSG00000163064), EN2 (ENSG00000164778), CPHXL (ENSG00000283755)

Protein

Protein identifiers

Cytoplasmic polyadenylated homeobox-like protein 2 — A0A1W2PPK0 (reviewed: A0A1W2PPK0)

All UniProt accessions (1): A0A1W2PPK0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (1): NP_001382791* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR050720	Engrailed_Homeobox_TFs	Family

Pfam: PF00046

UniProt features (5 total): compositionally biased region 2, chain 1, DNA-binding region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1W2PPK0-F1	51.33	0.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 6 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, chr16q23, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (3): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA binding (GO:0003677)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

180 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPHXL2	CUX2	O14529	247
CPHXL2	PLAC9	Q5JTB6	219
CPHXL2	TMEM254	Q8TBM7	204
CPHXL2	TIMM10	P62072	184
CPHXL2	TIMM44	O43615	178
CPHXL2	OCA2	Q04671	177
CPHXL2	TIMM13	P62206	167
CPHXL2	TIMM21	Q9BVV7	166
CPHXL2	SDHC	Q99643	166
CPHXL2	ALDH4A1	P30038	166
CPHXL2	NOL9	Q5SY16	166
CPHXL2	TIMM50	Q3ZCQ8	166
CPHXL2	SDHD	O14521	164
CPHXL2	DUXB	A0A1W2PPF3	163
CPHXL2	CHCHD4	Q8N4Q1	161

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GVQ3, A0A1W2PPK0, A0A1W2PPM1, A2A9I7, A6NCI8, A6QQS3, A7XCE8, E9PI22, E9PXT9, O15016, O91083, P09414, P0DMB1, P17923, P18804, P20879, P35965, P49750, Q0P670, Q12857, Q1RMX6, Q32LN6, Q32MG2, Q3B8N5, Q3T016, Q3V0A6, Q4JK59, Q5BI31, Q5T035, Q5ZKH6, Q642A3, Q6AXV6, Q6IMN6, Q6P1W5, Q6PEX7, Q6X4T0, Q80YD3, Q86UF4, Q8BII1, Q8C5V0

Diamond homologs: A0A1W2PPK0, A0A1W2PPM1, A1A546, A1YEY5, A1YFI3, A1YG57, A1YGA2, A2T733, A2T777, A2T7P4, A6NFQ7, G5EC89, L8E946, O14813, O15499, O35690, O42250, O42356, O42357, O42477, O70137, O73917, O75360, O95076, O97670, P0DMV5, P26367, P26630, P29454, P41935, P47237, P47238, P53544, P53545, P53546, P54366, P55813, P55864, P56915, P56916

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2647 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:75661241:G:C	F72L	0.995
16:75661241:G:T	F72L	0.995
16:75661243:A:G	F72L	0.995
16:75661242:A:G	F72S	0.993
16:75669477:A:C	F31L	0.993
16:75669477:A:T	F31L	0.993
16:75669479:A:G	F31L	0.993
16:75669454:A:G	L39P	0.989
16:75661244:C:A	W71C	0.984
16:75661244:C:G	W71C	0.984
16:75669478:A:G	F31S	0.984
16:75661246:A:G	W71R	0.983
16:75661246:A:T	W71R	0.983
16:75669387:A:C	F61L	0.983
16:75669387:A:T	F61L	0.983
16:75669389:A:G	F61L	0.983
16:75661229:T:A	R76S	0.978
16:75661229:T:G	R76S	0.978
16:75661242:A:C	F72C	0.977
16:75669478:A:C	F31C	0.977
16:75669454:A:T	L39H	0.976
16:75669397:G:T	A58D	0.975
16:75669398:C:G	A58P	0.975
16:75669408:C:A	R54S	0.971
16:75669408:C:G	R54S	0.971
16:75661221:A:G	L79P	0.967
16:75661245:C:G	W71S	0.966
16:75661243:A:C	F72V	0.965
16:75669417:G:C	F51L	0.964
16:75669417:G:T	F51L	0.964

dbSNP variants (sampled 300 via entrez): RS1000024016 (16:75666114 A>C), RS1000134974 (16:75660708 C>G,T), RS1000389850 (16:75659909 G>A,T), RS1000394111 (16:75660753 T>A,C), RS1000438257 (16:75670471 G>T), RS1000522772 (16:75674642 A>C), RS1000607965 (16:75674383 A>G), RS1000816075 (16:75669681 C>G), RS1000885592 (16:75664580 G>A), RS1000968613 (16:75664467 A>C), RS1001044982 (16:75669415 G>A), RS1001145059 (16:75664387 A>G), RS1001200153 (16:75666446 T>A,C), RS1001357469 (16:75661375 C>T), RS1001415586 (16:75669124 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)

Clinical trials (associated diseases)

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