NCBP2L

Summary

NCBP2L (nuclear cap binding protein subunit 2 like, HGNC:31795) is a protein-coding gene on chromosome Xq22.3, encoding Nuclear cap-binding protein subunit 2-like (A6PVI3).

Predicted to enable RNA cap binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of nuclear cap binding activity complex.

Source: NCBI Gene 392517 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001348372

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31795
Approved symbol	NCBP2L
Name	nuclear cap binding protein subunit 2 like
Location	Xq22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000170935
Ensembl biotype	protein_coding
Entrez	392517

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000509000, ENST00000639756, ENST00000893000

RefSeq mRNA: 1 — MANE Select: NM_001348372 NM_001348372

CCDS: CCDS87770

Canonical transcript exons

ENST00000509000 — 2 exons

Exon	Start	End
ENSE00002052816	107777733	107777858
ENSE00003938185	107794149	107795829

Expression profiles

Bgee: expression breadth broad, 71 present calls, max score 62.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	62.20	gold quality
right adrenal gland cortex	UBERON:0035827	61.72	gold quality
left adrenal gland	UBERON:0001234	61.05	gold quality
leukocyte	CL:0000738	60.99	gold quality
right adrenal gland	UBERON:0001233	60.84	gold quality
left adrenal gland cortex	UBERON:0035825	60.73	gold quality
adrenal gland	UBERON:0002369	59.74	gold quality
skeletal muscle tissue	UBERON:0001134	55.78	gold quality
adrenal tissue	UBERON:0018303	52.99	gold quality
muscle tissue	UBERON:0002385	52.71	silver quality
hindlimb stylopod muscle	UBERON:0004252	52.32	gold quality
gastrocnemius	UBERON:0001388	50.40	gold quality
muscle of leg	UBERON:0001383	50.34	gold quality
right ovary	UBERON:0002118	50.01	gold quality
islet of Langerhans	UBERON:0000006	49.86	gold quality
ovary	UBERON:0000992	49.49	gold quality
left ovary	UBERON:0002119	48.82	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	48.62	gold quality
bone marrow cell	CL:0002092	48.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	47.96	silver quality
left testis	UBERON:0004533	47.21	gold quality
right uterine tube	UBERON:0001302	47.12	gold quality
testis	UBERON:0000473	46.69	gold quality
tibial nerve	UBERON:0001323	46.49	gold quality
right testis	UBERON:0004534	46.25	gold quality
pancreas	UBERON:0001264	46.07	gold quality
saliva-secreting gland	UBERON:0001044	45.67	gold quality
minor salivary gland	UBERON:0001830	45.57	gold quality
tonsil	UBERON:0002372	44.26	gold quality
body of pancreas	UBERON:0001150	43.57	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.28

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ncbp2	ENSDARG00000014898
drosophila_melanogaster	Cbp20	FBGN0022943
caenorhabditis_elegans	ncbp-2	WBGENE00009141

Paralogs (1): NCBP2 (ENSG00000114503)

Protein

Protein identifiers

Nuclear cap-binding protein subunit 2-like — A6PVI3 (reviewed: A6PVI3)

All UniProt accessions (1): A6PVI3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the RRM NCBP2 family.

RefSeq proteins (1): NP_001335301* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR027157	NCBP2	Family
IPR034148	NCBP2_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6PVI3-F1	94.89	0.91

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): GOBP_RNA_SPLICING, GOBP_MRNA_CIS_SPLICING_VIA_SPLICEOSOME, GOCC_RNA_CAP_BINDING_COMPLEX, GOMF_RNA_CAP_BINDING, chrXq22, GOBP_MRNA_PROCESSING, GOCC_INTRACELLULAR_PROTEIN_CONTAINING_COMPLEX, HMGB2_TARGET_GENES, GOBP_MRNA_METABOLIC_PROCESS, GOBP_RNA_SPLICING_VIA_TRANSESTERIFICATION_REACTIONS, GSE40685_NAIVE_CD4_TCELL_VS_FOXP3_KO_TREG_PRECURSOR_DN, GOBP_RNA_PROCESSING

GO Biological Process (2): mRNA splicing, via spliceosome (GO:0000398), mRNA cis splicing, via spliceosome (GO:0045292)

GO Molecular Function (3): RNA cap binding (GO:0000339), nucleic acid binding (GO:0003676), RNA binding (GO:0003723)

GO Cellular Component (1): nuclear cap binding complex (GO:0005846)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA splicing, via spliceosome	1
RNA binding	1
binding	1
nucleic acid binding	1
RNA cap binding complex	1

Protein interactions and networks

STRING

1156 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NCBP2L	NCBP2AS2	Q69YL0	616
NCBP2L	NCBP1	Q09161	604
NCBP2L	EMC3	Q9P0I2	525
NCBP2L	RAB5C	P51148	493
NCBP2L	SF3B1	O75533	447
NCBP2L	KRAS	P01116	428
NCBP2L	VPS26B	Q4G0F5	419
NCBP2L	RPS27	P42677	384
NCBP2L	JADE3	Q92613	378
NCBP2L	KIF19	Q2TAC6	370
NCBP2L	ALDH18A1	P54886	366
NCBP2L	PSAT1	Q9Y617	361
NCBP2L	PPP2R3C	Q969Q6	360
NCBP2L	UBXN7	O94888	351
NCBP2L	XPO1	O14980	348

IntAct

116 interactions, top by confidence:

A	B	Type	Score
NCBP2L	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	WHRN	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
DLG2	NCBP2L	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	PDZK1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	RHPN1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	TAX1BP3	psi-mi:“MI:0407”(direct interaction)	0.440
DLG1	NCBP2L	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	ARHGEF12	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	GORASP2	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	SYNJ2BP	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	NOS1	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	GOPC	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	GRID2IP	psi-mi:“MI:0407”(direct interaction)	0.440
TIAM2	NCBP2L	psi-mi:“MI:0407”(direct interaction)	0.440
NCBP2L	MAGI1	psi-mi:“MI:0407”(direct interaction)	0.440

ESM2 similar proteins: A2SW84, A6PVI3, A8Y1R8, B0W939, B1WC40, B3LYP1, B3P0D7, B4GLK8, B4IBA4, B4JUT1, B4KCD5, B4LZ88, B4M205, B4NB54, B4PL68, B4QV17, B5G279, B7P877, C0H859, C1BY64, C6Y4C0, O94290, P25555, P36629, P40565, P52298, P52299, Q00916, Q05AT9, Q08920, Q177H0, Q1HE01, Q293V6, Q3ZBJ1, Q4IE79, Q54KR9, Q5ZKR5, Q6DES0, Q6FNF9, Q754W7

Diamond homologs: A0A0D1C8Z4, A2SW84, A6PVI3, A8Y1R8, B0W939, B1WC40, B3LYP1, B3P0D7, B4GLK8, B4IBA4, B4JUT1, B4KCD5, B4LZ88, B4M205, B4NB54, B4PL68, B4QV17, B5DGI7, B5G279, B7P877, C0H859, C0HFE5, C1BY64, O35698, O89086, P19684, P27476, P33240, P52298, P52299, P60824, P60825, P60826, P62995, P62996, P62997, P78795, P98179, Q05AT9, Q08920

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 75 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Ras activation upon Ca2+ influx through NMDA receptor	5	58.3×	9e-07
Unblocking of NMDA receptors, glutamate binding and activation	5	55.5×	9e-07
Negative regulation of NMDA receptor-mediated neuronal transmission	5	55.5×	9e-07
Long-term potentiation	5	48.5×	2e-06
Assembly and cell surface presentation of NMDA receptors	8	41.4×	1e-09
Neurexins and neuroligins	9	36.2×	4e-10
Protein-protein interactions at synapses	5	27.1×	3e-05
RHOA GTPase cycle	5	7.6×	5e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	88.8×	6e-17
protein localization to synapse	6	63.8×	4e-08
receptor clustering	7	60.7×	4e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	7	48.2×	2e-08
protein-containing complex assembly	9	14.2×	1e-06
cell-cell adhesion	9	12.7×	2e-06
regulation of small GTPase mediated signal transduction	5	10.0×	4e-03
protein localization to plasma membrane	5	7.5×	9e-03

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

233 predictions. Top by Δscore:

Variant	Effect	Δscore
X:107777909:A:T	donor_gain	0.9900
X:107794145:TTA:T	acceptor_loss	0.9800
X:107794146:TA:T	acceptor_loss	0.9800
X:107794147:A:AC	acceptor_loss	0.9800
X:107794148:G:GT	acceptor_loss	0.9800
X:107777912:G:GG	donor_gain	0.9700
X:107794137:A:AG	acceptor_gain	0.9700
X:107794142:A:AG	acceptor_gain	0.9700
X:107794330:A:T	donor_gain	0.9700
X:107794138:A:G	acceptor_gain	0.9600
X:107794146:TAGG:T	acceptor_gain	0.9600
X:107794147:A:AG	acceptor_gain	0.9600
X:107794148:G:GG	acceptor_gain	0.9600
X:107794148:GGT:G	acceptor_gain	0.9600
X:107777910:GA:G	donor_gain	0.9500
X:107794145:TTAG:T	acceptor_gain	0.9500
X:107794147:AG:A	acceptor_gain	0.9500
X:107794147:AGGT:A	acceptor_gain	0.9500
X:107794148:GG:G	acceptor_gain	0.9500
X:107794143:A:AG	acceptor_gain	0.9400
X:107777827:GCC:G	donor_gain	0.9300
X:107777911:A:AG	donor_gain	0.9300
X:107794139:C:G	acceptor_gain	0.9300
X:107794148:GGTTT:G	acceptor_gain	0.9300
X:107794144:C:G	acceptor_gain	0.9200
X:107794144:CTTA:C	acceptor_gain	0.9200
X:107794148:G:T	acceptor_gain	0.9200
X:107794148:GGTT:G	acceptor_gain	0.9200
X:107777857:AG:A	donor_loss	0.8800
X:107777858:GG:G	donor_loss	0.8800

AlphaMissense

1031 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:107794461:T:C	F81L	0.820
X:107794463:T:A	F81L	0.820
X:107794463:T:G	F81L	0.820
X:107794569:T:C	F117L	0.737
X:107794571:T:A	F117L	0.737
X:107794571:T:G	F117L	0.737
X:107794512:T:C	F98L	0.712
X:107794514:T:A	F98L	0.712
X:107794514:T:G	F98L	0.712
X:107794467:T:C	F83L	0.704
X:107794469:T:A	F83L	0.704
X:107794469:T:G	F83L	0.704
X:107794290:T:C	F24L	0.635
X:107794292:C:A	F24L	0.635
X:107794292:C:G	F24L	0.635
X:107794395:T:C	F59L	0.627
X:107794397:T:A	F59L	0.627
X:107794397:T:G	F59L	0.627
X:107794638:T:C	F140L	0.610
X:107794640:T:A	F140L	0.610
X:107794640:T:G	F140L	0.610
X:107794659:T:C	F147L	0.598
X:107794661:T:A	F147L	0.598
X:107794661:T:G	F147L	0.598
X:107794422:T:C	F68L	0.579
X:107794424:T:A	F68L	0.579
X:107794424:T:G	F68L	0.579
X:107794626:T:C	F136L	0.579
X:107794628:T:A	F136L	0.579
X:107794628:T:G	F136L	0.579

dbSNP variants (sampled 300 via entrez): RS1000427257 (X:107777176 C>A), RS1000439262 (X:107791895 G>A), RS1000565903 (X:107791251 T>C), RS1001530984 (X:107785408 C>T), RS1001840401 (X:107788231 G>A), RS1001983931 (X:107794893 T>C), RS1002235243 (X:107784886 G>T), RS1002509188 (X:107781263 T>A), RS1002610575 (X:107795539 A>G), RS1002982097 (X:107782936 C>A), RS1003195602 (X:107782881 A>T), RS1003514705 (X:107778465 C>T), RS1003541363 (X:107778946 G>A,C), RS1003789390 (X:107785943 A>G), RS1003872466 (X:107777698 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

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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