CENPVL3

Summary

CENPVL3 (centromere protein V like 3, HGNC:43880) is a protein-coding gene on chromosome Xp11.22, encoding Centromere protein V-like protein 3 (A0A0U1RRI6).

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

Source: NCBI Gene 347549 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001355276

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43880
Approved symbol	CENPVL3
Name	centromere protein V like 3
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000224109
Ensembl biotype	protein_coding
Entrez	347549

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000417339

RefSeq mRNA: 1 — MANE Select: NM_001355276 NM_001355276

CCDS: CCDS87743

Canonical transcript exons

ENST00000417339 — 1 exons

Exon	Start	End
ENSE00001769247	51617020	51618912

Expression profiles

Bgee: expression breadth broad, 49 present calls, max score 73.25.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0598 / max 6.3577, expressed in 23 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199307	0.0598	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	73.25	gold quality
nucleus accumbens	UBERON:0001882	69.55	gold quality
hypothalamus	UBERON:0001898	69.35	gold quality
ganglionic eminence	UBERON:0004023	64.99	gold quality
right testis	UBERON:0004534	62.47	gold quality
testis	UBERON:0000473	60.61	gold quality
left testis	UBERON:0004533	60.35	gold quality
prefrontal cortex	UBERON:0000451	60.34	gold quality
temporal lobe	UBERON:0001871	59.85	gold quality
amygdala	UBERON:0001876	59.75	gold quality
caudate nucleus	UBERON:0001873	59.24	gold quality
superior frontal gyrus	UBERON:0002661	58.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	58.43	gold quality
anterior cingulate cortex	UBERON:0009835	58.22	gold quality
putamen	UBERON:0001874	57.52	gold quality
Brodmann (1909) area 9	UBERON:0013540	56.45	gold quality
cerebral cortex	UBERON:0000956	56.27	gold quality
frontal cortex	UBERON:0001870	56.20	gold quality
Ammon’s horn	UBERON:0001954	55.92	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	55.42	gold quality
duodenum	UBERON:0002114	54.44	gold quality
brain	UBERON:0000955	52.75	gold quality
cortical plate	UBERON:0005343	52.33	gold quality
substantia nigra	UBERON:0002038	52.20	gold quality
right frontal lobe	UBERON:0002810	49.81	gold quality
primary visual cortex	UBERON:0002436	49.79	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	46.36	gold quality
adenohypophysis	UBERON:0002196	43.96	gold quality
pituitary gland	UBERON:0000007	38.66	gold quality
sural nerve	UBERON:0015488	38.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.54

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), CENPVL2 (ENSG00000283093)

Protein

Protein identifiers

Centromere protein V-like protein 3 — A0A0U1RRI6 (reviewed: A0A0U1RRI6)

Alternative names: Centromere protein V pseudogene 3

All UniProt accessions (1): A0A0U1RRI6

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_001342205* (*=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-A0A0U1RRI6-F1	73.03	0.42

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: 5 (showing top): GOMF_CARBON_SULFUR_LYASE_ACTIVITY, chrXp11, MEBARKI_HCC_PROGENITOR_WNT_UP, MEBARKI_HCC_PROGENITOR_WNT_UP_BLOCKED_BY_FZD8CRD, 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

52 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CENPVL3	CDCA3	Q99618	247
CENPVL3	MEI4	A8MW99	245
CENPVL3	CENPQ	Q7L2Z9	242
CENPVL3	CBX1	P23197	213
CENPVL3	ADORA2B	P29275	206
CENPVL3	SAXO4	Q7Z5V6	203
CENPVL3	CCDC181	Q5TID7	203
CENPVL3	HORMAD1	Q86X24	183
CENPVL3	RAD1	O60671	166
CENPVL3	ERGIC1	Q969X5	166
CENPVL3	CBX5	P45973	159
CENPVL3	ADORA2A	P29274	155
CENPVL3	CPN1	P15169	154
CENPVL3	ECHDC3	Q96DC8	154
CENPVL3	HORMAD2	Q8N7B1	154

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

157 predictions. Top by Δscore:

Variant	Effect	Δscore
X:51618749:TGG:T	donor_gain	0.8000
X:51618384:T:TA	donor_gain	0.6900
X:51618706:T:A	donor_gain	0.6900
X:51618252:TCTG:T	donor_gain	0.6500
X:51618253:CTGC:C	donor_gain	0.6500
X:51618222:C:CT	acceptor_gain	0.6200
X:51618329:C:CA	donor_gain	0.6200
X:51618712:C:CT	donor_gain	0.6000
X:51618161:T:TA	donor_gain	0.5800
X:51618552:T:A	donor_gain	0.5700
X:51618296:G:C	acceptor_gain	0.5200
X:51618439:C:CT	acceptor_gain	0.5100
X:51618713:C:CT	donor_gain	0.5100
X:51618200:CAG:C	acceptor_gain	0.4800
X:51618260:CCGCA:C	donor_loss	0.4800
X:51618261:CGCA:C	donor_loss	0.4800
X:51618262:GCA:G	donor_loss	0.4800
X:51618263:CA:C	donor_loss	0.4800
X:51618264:AC:A	donor_loss	0.4800
X:51618265:C:CG	donor_loss	0.4800
X:51618266:C:A	donor_loss	0.4800
X:51618196:C:CT	acceptor_gain	0.4600
X:51618265:CCTG:C	donor_gain	0.4600
X:51618693:T:TA	donor_gain	0.4600
X:51618057:A:AC	donor_gain	0.4500
X:51618058:C:CC	donor_gain	0.4500
X:51618267:T:C	donor_loss	0.4400
X:51618157:G:T	donor_gain	0.4300
X:51618202:G:GC	acceptor_gain	0.4300
X:51618268:G:A	donor_gain	0.4300

AlphaMissense

1840 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:51618274:G:C	F215L	0.997
X:51618274:G:T	F215L	0.997
X:51618276:A:G	F215L	0.997
X:51618344:A:G	F192S	0.997
X:51618442:A:C	F159L	0.997
X:51618442:A:T	F159L	0.997
X:51618444:A:G	F159L	0.997
X:51618247:G:C	F224L	0.996
X:51618247:G:T	F224L	0.996
X:51618249:A:G	F224L	0.996
X:51618443:A:G	F159S	0.995
X:51618250:A:C	S223R	0.993
X:51618250:A:T	S223R	0.993
X:51618252:T:G	S223R	0.993
X:51618443:A:C	F159C	0.993
X:51618365:A:G	F185S	0.991
X:51618343:G:C	F192L	0.990
X:51618343:G:T	F192L	0.990
X:51618345:A:G	F192L	0.990
X:51618248:A:G	F224S	0.989
X:51618263:C:G	C219S	0.988
X:51618264:A:T	C219S	0.988
X:51618477:G:C	H148D	0.987
X:51618565:C:A	W118C	0.987
X:51618565:C:G	W118C	0.987
X:51618458:C:T	C154Y	0.986
X:51618212:A:T	V236D	0.985
X:51618272:C:T	C216Y	0.985
X:51618464:C:G	C152S	0.985
X:51618465:A:T	C152S	0.985

dbSNP variants (sampled 300 via entrez): RS1001192050 (X:51617080 A>G), RS1002842752 (X:51616538 A>G), RS1003268772 (X:51620445 G>A), RS1006948656 (X:51619350 A>C), RS1007453011 (X:51620000 T>C), RS1011495309 (X:51620501 C>T), RS1011612168 (X:51617209 C>T), RS1011878726 (X:51620855 G>A), RS1021093355 (X:51617219 A>G), RS1021229353 (X:51617566 G>A), RS1021434084 (X:51620514 A>G), RS1021498331 (X:51620177 G>C,T), RS1025559239 (X:51620093 C>T), RS1025631414 (X:51619520 G>A), RS1029770785 (X:51617336 C>G,T)

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.