CENPVL2

Summary

CENPVL2 (centromere protein V like 2, HGNC:43879) is a protein-coding gene on chromosome Xp11.22, encoding Centromere protein V-like protein 2 (P0DPI3).

Predicted to enable carbon-sulfur lyase activity and metal ion binding activity.

Source: NCBI Gene 441495 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total — 1 likely-pathogenic
• MANE Select transcript: NM_001355278

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43879
Approved symbol	CENPVL2
Name	centromere protein V like 2
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283093
Ensembl biotype	protein_coding
Entrez	441495

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000634648

RefSeq mRNA: 1 — MANE Select: NM_001355278 NM_001355278

CCDS: CCDS87744

Canonical transcript exons

ENST00000634648 — 1 exons

Exon	Start	End
ENSE00003788822	51681212	51682831

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 69.23.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	69.23	gold quality
ventricular zone	UBERON:0003053	66.08	gold quality
hypothalamus	UBERON:0001898	64.23	gold quality
nucleus accumbens	UBERON:0001882	63.55	gold quality
ganglionic eminence	UBERON:0004023	58.46	gold quality
prefrontal cortex	UBERON:0000451	56.75	gold quality
caudate nucleus	UBERON:0001873	56.71	gold quality
putamen	UBERON:0001874	55.58	gold quality
frontal cortex	UBERON:0001870	49.74	gold quality
temporal lobe	UBERON:0001871	48.82	gold quality
substantia nigra	UBERON:0002038	48.69	gold quality
amygdala	UBERON:0001876	48.53	gold quality
brain	UBERON:0000955	47.93	gold quality
cerebral cortex	UBERON:0000956	47.35	gold quality
superior frontal gyrus	UBERON:0002661	46.97	silver quality
Brodmann (1909) area 9	UBERON:0013540	46.67	gold quality
anterior cingulate cortex	UBERON:0009835	46.30	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	45.05	gold quality
Ammon’s horn	UBERON:0001954	44.77	gold quality
gall bladder	UBERON:0002110	43.13	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	41.03	gold quality
right frontal lobe	UBERON:0002810	39.88	gold quality
bone marrow cell	CL:0002092	38.74	gold quality
lower esophagus mucosa	UBERON:0035834	37.73	gold quality
pituitary gland	UBERON:0000007	37.64	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
right testis	UBERON:0004534	37.20	gold quality
duodenum	UBERON:0002114	36.62	gold quality
sural nerve	UBERON:0015488	35.00	gold quality
adenohypophysis	UBERON:0002196	34.99	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.27

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	cenpv	ENSDARG00000092285
caenorhabditis_elegans		WBGENE00017771

Paralogs (3): CENPV (ENSG00000166582), CENPVL1 (ENSG00000223591), CENPVL3 (ENSG00000224109)

Protein

Protein identifiers

Centromere protein V-like protein 2 — P0DPI3 (reviewed: P0DPI3)

Alternative names: Centromere protein V pseudogene 2

All UniProt accessions (1): P0DPI3

UniProt curated annotations — full annotation on UniProt →

Cofactor. Binds 2 Zn(2+) ions per subunit.

Similarity. Belongs to the Gfa family.

RefSeq proteins (1): NP_001342207* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006913	CENP-V/GFA	Domain
IPR011057	Mss4-like_sf	Homologous_superfamily
IPR052355	CENP-V-like	Family

Pfam: PF04828

UniProt features (14 total): binding site 7, region of interest 3, compositionally biased region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DPI3-F1	71.90	0.38

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (7): 159; 162; 201; 204; 137; 139; 157

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): GOMF_CARBON_SULFUR_LYASE_ACTIVITY, chrXp11, GOMF_LYASE_ACTIVITY

GO Biological Process (0):

GO Molecular Function (2): carbon-sulfur lyase activity (GO:0016846), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lyase activity	1
cation binding	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0U1RR11, A0A0U1RRI6, A6NCS6, A6NJG2, B0BN44, D3YXK1, E9PY61, E9Q0B3, F5H4A9, O00220, O00221, P09038, P0DPI3, P22083, P98077, Q08AU9, Q2M2W7, Q2M3V2, Q2TBI2, Q5F267, Q5FW56, Q5IS69, Q5R866, Q5T4W7, Q5TM52, Q5U4P2, Q5VTJ3, Q659K9, Q673H1, Q69ZB3, Q6AYE8, Q6IPT2, Q6PJ61, Q7RTU4, Q7TSX9, Q7YR31, Q80SU3, Q86SH2, Q86Y97, Q8NBR0

Diamond homologs: A0A0U1RR11, A0A0U1RRI6, E1VBT6, P0DPI3, Q7Z7K6, Q9CXS4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
4075824	Single allele	Likely pathogenic

SpliceAI

129 predictions. Top by Δscore:

Variant	Effect	Δscore
X:51682707:TGG:T	donor_gain	0.5700
X:51682180:C:CT	acceptor_gain	0.4800
X:51681713:CAA:C	acceptor_gain	0.4600
X:51681787:CCGAA:C	donor_gain	0.4600
X:51681811:C:CT	donor_gain	0.4600
X:51681812:T:TT	donor_gain	0.4600
X:51681716:C:CC	acceptor_gain	0.4300
X:51682342:T:TA	donor_gain	0.4300
X:51682670:C:CT	donor_gain	0.4300
X:51681782:CCTTA:C	donor_loss	0.4200
X:51681783:CTT:C	donor_loss	0.4200
X:51681784:TTA:T	donor_loss	0.4200
X:51681785:T:TG	donor_loss	0.4200
X:51681786:AC:A	donor_loss	0.4200
X:51682119:T:TA	donor_gain	0.4200
X:51682510:T:TA	donor_gain	0.4100
X:51682210:TCTG:T	donor_gain	0.3700
X:51682211:CTGC:C	donor_gain	0.3700
X:51681781:T:TA	donor_gain	0.3600
X:51682174:CG:C	acceptor_gain	0.3600
X:51682665:CCCAG:C	donor_gain	0.3600
X:51682666:CCAGC:C	donor_gain	0.3600
X:51682667:CAGCC:C	donor_gain	0.3600
X:51682668:AGCCA:A	donor_gain	0.3600
X:51681715:ACTG:A	acceptor_gain	0.3400
X:51681716:CTGT:C	acceptor_gain	0.3400
X:51682175:G:C	acceptor_gain	0.3400
X:51682671:C:CT	donor_gain	0.3400
X:51681714:AACT:A	acceptor_gain	0.3300
X:51681788:C:A	donor_loss	0.3300

AlphaMissense

1741 scored. Top likely-pathogenic:

dbSNP variants (sampled 29 via entrez): RS1557345761 (X:51682441 C>T), RS1557345762 (X:51682504 G>A), RS1557345763 (X:51682508 C>T), RS1557345764 (X:51682543 C>G), RS1557345766 (X:51682566 G>A), RS1557345768 (X:51682585 C>A), RS1557345769 (X:51682653 C>G), RS1557345770 (X:51682740 G>A), RS1569554708 (X:51682845 T>G), RS1569554709 (X:51683038 A>G), RS1602174266 (X:51682117 C>A), RS1602174269 (X:51682402 A>G), RS1602174273 (X:51682462 T>C), RS1602174280 (X:51682514 G>A), RS1602174286 (X:51682561 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:300009, MIM:300554, MIM:308990, MIM:310468

GenCC curated gene-disease

Mondo (4): Dent disease type 1 (MONDO:0010225), hypophosphatemic rickets, X-linked recessive (MONDO:0010358), proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis (MONDO:0010644), nephrolithiasis, X-linked recessive, with renal failure (MONDO:0010687)

Orphanet (2): Dent disease (Orphanet:1652), Dent disease type 1 (Orphanet:93622)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C545036	Low Molecular Weight Proteinuria with Hypercalciuria and Nephrocalcinosis (supp.)
C562901	Nephrolithiasis, X-Linked Recessive, with Renal Failure (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Sunitinib	decreases expression	1

Clinical trials (associated diseases)

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