UBN1

ubinuclein 1, the group of HIRA histone chaperone complex subunits|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 16:4846664-4882401

Links

ENSG00000118900 ∙ NCBI:29855 ∙ OMIM:609771 ∙ HGNC:12506 ∙ Uniprot:Q9NPG3 ∙ 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 UBN1 gene.

• not provided (13 variants)
• Non-immune hydrops fetalis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBN1 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				4	5	9
missense		1			3	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	1	0	4	8

Highest pathogenic variant AF is 0.0000131

Variants in UBN1

This is a list of pathogenic ClinVar variants found in the UBN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4858609-C-T			Likely benign (May 30, 2018)
16-4860860-C-G			Benign (Jul 27, 2018)
16-4870840-G-A			Benign (Dec 31, 2019)
16-4871164-G-C			Likely benign (Jun 13, 2018)
16-4874279-G-C			Benign (Sep 11, 2018)
16-4874333-C-T			Benign (Jun 13, 2018)
16-4874426-G-A			Benign (Sep 11, 2018)
16-4874766-T-A		Non-immune hydrops fetalis	Likely pathogenic (Apr 29, 2013)
16-4874904-G-C			Benign (Dec 31, 2019)
16-4874984-A-G			Likely benign (Jul 23, 2018)
16-4875083-A-C			Benign (Dec 31, 2019)
16-4876957-C-T			Likely benign (Jul 01, 2022)
16-4877083-C-T			Benign (Jul 23, 2018)
16-4877461-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBN1	protein_coding	protein_coding	ENST00000396658	17	35696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000530	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.789	691	635	1.09	0.0000363	7332
Missense in Polyphen		193	230.98	0.83557		2731
Synonymous	-3.14	335	269	1.24	0.0000169	2341
Loss of Function	5.89	5	49.9	0.100	0.00000276	610

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)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a novel regulator of senescence. Involved in the formation of senescence-associated heterochromatin foci (SAHF), which represses expression of proliferation-promoting genes. Binds to proliferation-promoting genes. May be required for replication- independent chromatin assembly. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:19029251}.
• Pathway: Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• rvis_EVS: -1.7
• rvis_percentile_EVS: 2.59

Haploinsufficiency Scores

• pHI: 0.0939
• hipred: Y
• hipred_score: 0.590
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubn1

Gene ontology

• Biological process: DNA replication-independent nucleosome assembly;regulation of transcription by RNA polymerase II;viral process
• Cellular component: nucleus;nucleoplasm;bicellular tight junction;nuclear body;PML body
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding