NCBP3

nuclear cap binding subunit 3

Basic information

Region (hg38): 17:3802157-3846246

Previous symbols: [ "C17orf85" ]

Links

ENSG00000074356 ∙ NCBI:55421 ∙ OMIM:616624 ∙ HGNC:24612 ∙ Uniprot:Q53F19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NCBP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCBP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in NCBP3

This is a list of pathogenic ClinVar variants found in the NCBP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-3813073-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-3813220-C-T		not specified	Uncertain significance (Nov 30, 2021)
17-3814327-T-C		not specified	Uncertain significance (Oct 26, 2022)
17-3814337-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-3814447-G-A		not specified	Uncertain significance (Nov 17, 2022)
17-3816127-C-A		not specified	Uncertain significance (Dec 07, 2023)
17-3816160-C-T		not specified	Uncertain significance (Oct 31, 2023)
17-3816207-T-A		not specified	Uncertain significance (Mar 16, 2022)
17-3816241-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-3818302-A-G		not specified	Uncertain significance (Apr 23, 2024)
17-3818366-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-3818426-G-A		not specified	Likely benign (Mar 29, 2022)
17-3821257-C-T		not specified	Uncertain significance (Mar 15, 2024)
17-3821269-G-A		not specified	Uncertain significance (Dec 19, 2023)
17-3821333-G-A		not specified	Uncertain significance (Nov 19, 2022)
17-3822001-T-A		not specified	Uncertain significance (Mar 29, 2022)
17-3822008-T-C		not specified	Uncertain significance (Oct 02, 2023)
17-3825038-A-C		not specified	Uncertain significance (Dec 06, 2023)
17-3825043-G-A		not specified	Uncertain significance (Oct 05, 2023)
17-3825835-C-T		not specified	Uncertain significance (Oct 05, 2022)
17-3826119-C-G		not specified	Uncertain significance (Sep 16, 2021)
17-3829340-G-C		not specified	Uncertain significance (Dec 17, 2023)
17-3843109-T-C		not specified	Uncertain significance (Mar 01, 2023)
17-3846044-G-C		not specified	Uncertain significance (Mar 06, 2023)
17-3846060-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCBP3	protein_coding	protein_coding	ENST00000389005	13	35086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000513	125744	0	3	125747	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.32	232	355	0.654	0.0000211	4074
Missense in Polyphen		88	134.06	0.6564		1480
Synonymous	-0.114	133	131	1.01	0.00000801	1145
Loss of Function	5.02	3	35.0	0.0856	0.00000223	408

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with NCBP1/CBP80 to form an alternative cap- binding complex (CBC) which plays a key role in mRNA export. NCBP3 serves as adapter protein linking the capped RNAs (m7GpppG-capped RNA) to NCBP1/CBP80. Unlike the conventional CBC with NCBP2 which binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus, the alternative CBC with NCBP3 does not bind snRNA and associates only with mRNA thereby playing a role in only mRNA export. The alternative CBC is particularly important in cellular stress situations such as virus infections and the NCBP3 activity is critical to inhibit virus growth (PubMed:26382858). {ECO:0000269|PubMed:26382858}.

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.783
• ghis: 0.463

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ncbp3
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: 7-methylguanosine mRNA capping;mRNA transport;defense response to virus
• Cellular component: nucleus;cytoplasm;nuclear speck;RNA cap binding complex
• Molecular function: RNA 7-methylguanosine cap binding;RNA binding;mRNA binding;protein binding