UBN2

protein-coding

ubinuclein 2

Gene summary

Predicted to be involved in chromatin organization. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_173569.4

Inheritance

—

ClinVar variants

P:1U:205B:22

Top phenotype

UBN2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr7:139,230,356-139,308,236

External References & Databases

Ensembl (ENSG00000157741)

Transcript & Mutation Effects

hg38 • Region Span ~77.9 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 UBN2 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 195

UBN2-related disorderTotal: 21

not providedTotal: 10

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Autism spectrum disorderTotal: 1

UBN2 associated Autism susceptibilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173569.4. 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	Sum
synonymous				6 clinvar	4 clinvar	10
missense			203 clinvar	6 clinvar	6 clinvar	215
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	0	1	205	12	10	228

Highest pathogenic variant AF is 6.8447486e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173569.4	RefSeq	NP_775840.3	18	MANE Select
ENST00000473989.8	Ensembl	ENSP00000418648.2	18	MANE Select
ENST00000483726.1	Ensembl	ENSP00000417846.1	9	Standard
ENST00000486663.5	Ensembl	ENSP00000417849.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular space
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000473989
Coding exons: 18
Length: 77881
Individuals with no LoFs: 124768
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 124796
p: 0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.187	657	671	0.980	0.0000348	8627
Missense (PolyPhen)		274	343.33	0.79805		4409
Synonymous	-1.10	281	258	1.09	0.0000135	2821
Loss of Function	5.85	5	49.3	0.101	0.00000230	693

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00084	0.00084	rare
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0982

Intolerance Scores

LoFtool: 0.283
RVIS EVS: -0.55
RVIS percentile EVS: 20

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.449

Gene Damage Prediction

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