UBN2

ubinuclein 2

Basic information

Region (hg38): 7:139230356-139308236

Links

ENSG00000157741 ∙ NCBI:254048 ∙ OMIM:613841 ∙ HGNC:21931 ∙ Uniprot:Q6ZU65 ∙ 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 UBN2 gene.

• not_specified (179 variants)
• UBN2-related_disorder (21 variants)
• not_provided (10 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Autism_spectrum_disorder (1 variants)
• UBN2_associated_Autism_susceptibility (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173569.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	4	10
missense			182	5	6	193
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1				1
Total	0	1	183	11	10

Highest pathogenic variant AF is 6.8447486e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBN2	protein_coding	protein_coding	ENST00000473989	18	77881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000673	124768	0	28	124796	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.187	657	671	0.980	0.0000348	8627
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000932	0.000928
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000468	0.0000464
European (Non-Finnish)	0.0000621	0.0000618
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.000334	0.000330

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• loftool: 0.283
• rvis_EVS: -0.55
• rvis_percentile_EVS: 20

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.387
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.449

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubn2

Gene ontology

• Cellular component: extracellular space;nucleoplasm