CENPVL1

Summary

CENPVL1 (centromere protein V like 1, HGNC:31851) is a protein-coding gene on chromosome Xp11.22, encoding Centromere protein V-like protein 1 (A0A0U1RR11).

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

Source: NCBI Gene 389857 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001355277

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31851
Approved symbol	CENPVL1
Name	centromere protein V like 1
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	PRR6L1
Ensembl gene	ENSG00000223591
Ensembl biotype	protein_coding
Entrez	389857

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000602548

RefSeq mRNA: 1 — MANE Select: NM_001355277 NM_001355277

CCDS: CCDS87745

Canonical transcript exons

ENST00000602548 — 1 exons

Exon	Start	End
ENSE00003264129	51710512	51712131

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 59.05.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	59.05	silver quality
ventricular zone	UBERON:0003053	58.76	silver quality
putamen	UBERON:0001874	57.11	gold quality
hypothalamus	UBERON:0001898	55.57	gold quality
nucleus accumbens	UBERON:0001882	54.78	gold quality
caudate nucleus	UBERON:0001873	54.53	gold quality
temporal lobe	UBERON:0001871	47.43	gold quality
amygdala	UBERON:0001876	47.39	gold quality
gall bladder	UBERON:0002110	45.70	gold quality
substantia nigra	UBERON:0002038	45.16	gold quality
Brodmann (1909) area 9	UBERON:0013540	44.52	gold quality
brain	UBERON:0000955	44.07	gold quality
frontal cortex	UBERON:0001870	43.99	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	43.47	gold quality
cerebral cortex	UBERON:0000956	43.19	gold quality
superior frontal gyrus	UBERON:0002661	42.31	gold quality
anterior cingulate cortex	UBERON:0009835	41.35	gold quality
Ammon’s horn	UBERON:0001954	40.74	gold quality
duodenum	UBERON:0002114	39.28	gold quality
right frontal lobe	UBERON:0002810	39.13	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	37.87	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
lower esophagus mucosa	UBERON:0035834	36.76	gold quality
primary visual cortex	UBERON:0002436	36.24	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	35.38	gold quality
vermiform appendix	UBERON:0001154	34.80	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
mucosa of stomach	UBERON:0001199	33.20	gold quality
lymph node	UBERON:0000029	32.30	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.30

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), CENPVL3 (ENSG00000224109), CENPVL2 (ENSG00000283093)

Protein

Protein identifiers

Centromere protein V-like protein 1 — A0A0U1RR11 (reviewed: A0A0U1RR11)

Alternative names: Centromere protein V pseudogene 1

All UniProt accessions (1): A0A0U1RR11

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_001342206* (*=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-A0A0U1RR11-F1	70.33	0.31

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

90 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CENPVL1	GSPT2	Q8IYD1	662
CENPVL1	MAGED1	Q9Y5V3	516
CENPVL1	SHROOM4	Q9ULL8	507
CENPVL1	FAM120C	Q9NX05	480
CENPVL1	TSPYL2	Q9H2G4	419
CENPVL1	IQSEC2	Q5JU85	416
CENPVL1	PHF8	Q9UPP1	322
CENPVL1	KDM5C	P41229	280
CENPVL1	SLFN12	Q8IYM2	263
CENPVL1	HUWE1	Q7Z6Z7	259
CENPVL1	ACOT9	Q9Y305	251
CENPVL1	CDCA3	Q99618	247
CENPVL1	MEI4	A8MW99	245
CENPVL1	CENPQ	Q7L2Z9	242
CENPVL1	MTRFR	Q9H3J6	223

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

133 predictions. Top by Δscore:

Variant	Effect	Δscore
X:51710633:TCC:T	donor_gain	0.5500
X:51711162:C:CA	acceptor_gain	0.4800
X:51711530:T:TA	donor_gain	0.4600
X:51711531:A:AA	donor_gain	0.4600
X:51711551:ATTCG:A	donor_gain	0.4600
X:51711627:GTT:G	acceptor_gain	0.4600
X:51710832:G:GT	donor_gain	0.4400
X:51710672:G:GA	donor_gain	0.4300
X:51711000:G:GT	donor_gain	0.4300
X:51711626:A:AG	acceptor_gain	0.4300
X:51711627:G:GG	acceptor_gain	0.4300
X:51711553:TCG:T	donor_loss	0.4200
X:51711554:CGG:C	donor_loss	0.4200
X:51711555:GGTA:G	donor_loss	0.4200
X:51711556:G:GC	donor_loss	0.4200
X:51711557:T:A	donor_loss	0.4200
X:51711223:G:GT	donor_gain	0.4100
X:51711558:AAG:A	donor_loss	0.4000
X:51711128:TGCA:T	donor_gain	0.3700
X:51711129:GCAG:G	donor_gain	0.3700
X:51711167:AC:A	acceptor_gain	0.3600
X:51710670:GTGGC:G	donor_gain	0.3500
X:51710671:TGGCT:T	donor_gain	0.3500
X:51710673:GCTGG:G	donor_gain	0.3500
X:51711561:G:GT	donor_gain	0.3500
X:51711168:C:G	acceptor_gain	0.3400
X:51711623:TACA:T	acceptor_gain	0.3400
X:51711624:ACAG:A	acceptor_gain	0.3400
X:51711055:G:GT	donor_gain	0.3300
X:51711182:ACT:A	acceptor_gain	0.3300

AlphaMissense

1741 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:51711109:T:C	F200L	0.999
X:51711111:C:A	F200L	0.999
X:51711111:C:G	F200L	0.999
X:51710941:T:C	F144L	0.998
X:51710943:T:A	F144L	0.998
X:51710943:T:G	F144L	0.998
X:51711041:T:C	F177S	0.998
X:51711136:T:C	F209L	0.998
X:51711138:C:A	F209L	0.998
X:51711138:C:G	F209L	0.998
X:51710942:T:C	F144S	0.997
X:51711133:A:C	S208R	0.996
X:51711135:T:A	S208R	0.996
X:51711135:T:G	S208R	0.996
X:51710942:T:G	F144C	0.995
X:51710908:C:G	H133D	0.994
X:51710927:G:A	C139Y	0.994
X:51711020:T:C	F170S	0.994
X:51711040:T:C	F177L	0.994
X:51711042:C:A	F177L	0.994
X:51711042:C:G	F177L	0.994
X:51711113:G:A	C201Y	0.994
X:51711121:T:A	C204S	0.994
X:51711122:G:C	C204S	0.994
X:51711137:T:C	F209S	0.994
X:51710820:G:C	W103C	0.993
X:51710820:G:T	W103C	0.993
X:51710920:T:C	C137R	0.993
X:51710936:T:A	V142D	0.993
X:51711125:G:A	G205E	0.993

dbSNP variants (sampled 94 via entrez): RS1557347401 (X:51710365 G>C), RS1557347402 (X:51710374 A>G), RS1557347405 (X:51710416 G>T), RS1557347407 (X:51710521 G>C), RS1557347409 (X:51710546 G>T), RS1557347411 (X:51710552 G>C), RS1557347412 (X:51710560 C>A), RS1557347414 (X:51710564 C>T), RS1557347416 (X:51710669 G>A,C), RS1557347420 (X:51710690 G>C), RS1557347423 (X:51710700 C>G), RS1557347425 (X:51710708 G>C), RS1557347426 (X:51710730 A>G), RS1557347427 (X:51710752 A>C), RS1557347430 (X:51710753 C>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)

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
butyraldehyde	increases expression	1
Valproic Acid	increases expression	1

Clinical trials (associated diseases)

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