CPHXL

Summary

CPHXL (cytoplasmic polyadenylated homeobox like, HGNC:51815) is a protein-coding gene on chromosome 16q23.1, encoding Cytoplasmic polyadenylated homeobox-like protein (A0A1W2PPM1). Transcription factor that acts as activator.

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 105371346 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_001355613

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51815
Approved symbol	CPHXL
Name	cytoplasmic polyadenylated homeobox like
Location	16q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283755
Ensembl biotype	protein_coding
OMIM	618700
Entrez	105371346

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000640559

RefSeq mRNA: 1 — MANE Select: NM_001355613 NM_001355613

CCDS: CCDS86543

Canonical transcript exons

ENST00000640559 — 3 exons

Exon	Start	End
ENSE00003802873	75718265	75718458
ENSE00003806107	75714131	75715222
ENSE00003806470	75726418	75726490

Expression profiles

Bgee: expression breadth tissue_specific, 5 present calls, max score 51.77.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	51.77	silver quality
colonic epithelium	UBERON:0000397	47.47	gold quality
bone marrow cell	CL:0002092	47.06	gold quality
corpus callosum	UBERON:0002336	45.48	silver quality
skeletal muscle tissue	UBERON:0001134	44.88	gold quality
muscle tissue	UBERON:0002385	39.51	gold quality
tonsil	UBERON:0002372	38.32	gold quality
bone marrow	UBERON:0002371	37.31	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.83	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
cortex of kidney	UBERON:0001225	33.58	gold quality
mucosa of stomach	UBERON:0001199	32.93	gold quality
liver	UBERON:0002107	31.30	gold quality
urinary bladder	UBERON:0001255	31.07	gold quality
metanephros cortex	UBERON:0010533	30.74	gold quality
primary visual cortex	UBERON:0002436	30.52	gold quality
kidney	UBERON:0002113	30.40	gold quality
testis	UBERON:0000473	30.00	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
left testis	UBERON:0004533	29.79	silver quality
vermiform appendix	UBERON:0001154	29.45	gold quality
blood	UBERON:0000178	29.33	gold quality
uterine cervix	UBERON:0000002	29.12	gold quality
lymph node	UBERON:0000029	28.87	gold quality
popliteal artery	UBERON:0002250	28.18	gold quality
tibial artery	UBERON:0007610	28.15	gold quality
duodenum	UBERON:0002114	28.14	gold quality
thyroid gland	UBERON:0002046	27.98	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-36552	yes	817.01
E-ANND-3	no	2.11

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), CPHXL2 (ENSG00000284484)

Protein

Protein identifiers

Cytoplasmic polyadenylated homeobox-like protein — A0A1W2PPM1 (reviewed: A0A1W2PPM1)

Alternative names: Cytoplasmic polyadenylated homeobox 1

All UniProt accessions (1): A0A1W2PPM1

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that acts as activator.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_001342542* (*=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 (7 total): compositionally biased region 3, region of interest 2, chain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1W2PPM1-F1	50.79	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WONG_ADULT_TISSUE_STEM_MODULE, 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

178 interactions, top by confidence (×1000):

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	7
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2682 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:75715214:G:C	F76L	0.997
16:75715214:G:T	F76L	0.997
16:75715216:A:G	F76L	0.997
16:75718379:A:C	F35L	0.996
16:75718379:A:T	F35L	0.996
16:75718381:A:G	F35L	0.996
16:75715215:A:G	F76S	0.994
16:75718380:A:G	F35S	0.994
16:75715219:A:G	W75R	0.993
16:75715219:A:T	W75R	0.993
16:75718310:C:A	R58S	0.992
16:75718310:C:G	R58S	0.992
16:75718356:A:G	L43P	0.992
16:75715217:C:A	W75C	0.991
16:75715217:C:G	W75C	0.991
16:75718299:G:T	A62D	0.991
16:75718300:C:G	A62P	0.991
16:75718380:A:C	F35C	0.989
16:75718302:A:G	L61P	0.987
16:75715215:A:C	F76C	0.983
16:75715218:C:G	W75S	0.983
16:75718343:A:C	F47L	0.983
16:75718343:A:T	F47L	0.983
16:75718345:A:G	F47L	0.983
16:75715194:A:G	L83P	0.981
16:75715202:T:A	R80S	0.979
16:75715202:T:G	R80S	0.979
16:75718289:A:C	F65L	0.979
16:75718289:A:T	F65L	0.979
16:75718291:A:G	F65L	0.979

dbSNP variants (sampled 300 via entrez): RS1000118828 (16:75724298 T>C), RS1000252403 (16:75728296 T>A,C), RS1000283540 (16:75728085 T>C), RS1000331942 (16:75716135 T>C), RS1000422809 (16:75727704 C>A,G,T), RS1000475054 (16:75727950 A>G), RS1000596690 (16:75724113 A>C,G,T), RS1000694658 (16:75715763 C>T), RS1000917429 (16:75717250 C>A), RS1000961994 (16:75721365 G>A,C), RS1001195576 (16:75727040 A>G), RS1001264911 (16:75717444 G>A,T), RS1001525450 (16:75725128 G>T), RS1001691683 (16:75714510 C>G), RS1001700711 (16:75719587 G>A,C)

Disease associations

OMIM: gene MIM:618700 | 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.