NCBP2L

protein-coding

nuclear cap binding protein subunit 2 like, the group of RNA binding motif containing

Gene summary

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. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001348372.2

Inheritance

—

ClinVar variants

—

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:107,774,899-107,795,829

External References & Databases

Ensembl (ENSG00000170935)

Transcript & Mutation Effects

hg38 • Region Span ~20.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NCBP2L variants in ClinVar

1 Conditions Cataloged

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001348372.2	RefSeq	NP_001335301.1	1	MANE Select
ENST00000509000.3	Ensembl	ENSP00000476955.1	1	MANE Select
ENST00000639756.1	Ensembl	ENSP00000492033.1	1	Standard
ENST00000893000.1	Ensembl	ENSP00000563059.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splicing, via spliceosome
mRNA cis splicing, via spliceosome

Molecular Function

RNA cap binding

Cellular Component

nuclear cap binding complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000509000
Coding exons: 1
Length: 16950

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0622	61	59.6	1.02	0.00000460	1029
Missense (PolyPhen)		19	18.093	1.0501		312
Synonymous	-0.848	26	21.0	1.24	0.00000154	275
Loss of Function

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.121

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium