UBAP2

ubiquitin associated protein 2, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 9:33921693-34049388

Links

ENSG00000137073 ∙ NCBI:55833 ∙ ∙ HGNC:14185 ∙ Uniprot:Q5T6F2 ∙ 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 UBAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBAP2 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				1		1
missense			96	7	2	105
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	96	8	2

Variants in UBAP2

This is a list of pathogenic ClinVar variants found in the UBAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-33922517-T-G		not specified	Uncertain significance (Mar 25, 2024)
9-33922527-T-A		not specified	Uncertain significance (May 02, 2024)
9-33922584-G-A		not specified	Uncertain significance (Nov 03, 2022)
9-33922599-T-A		not specified	Uncertain significance (Apr 09, 2024)
9-33922763-G-A		not specified	Uncertain significance (Oct 29, 2024)
9-33922793-G-A		not specified	Uncertain significance (Sep 30, 2024)
9-33922874-A-C		not specified	Uncertain significance (Jan 31, 2022)
9-33922875-A-G		not specified	Uncertain significance (Jul 25, 2023)
9-33922976-T-C		not specified	Uncertain significance (Feb 23, 2023)
9-33922977-T-C		not specified	Uncertain significance (Jan 30, 2024)
9-33922997-T-C		not specified	Uncertain significance (Aug 28, 2024)
9-33923015-C-T		not specified	Uncertain significance (Jun 04, 2024)
9-33923203-C-T		not specified	Uncertain significance (Dec 03, 2021)
9-33923251-G-A		not specified	Uncertain significance (Apr 19, 2023)
9-33923408-C-G		not specified	Uncertain significance (Feb 06, 2023)
9-33923811-T-C		not specified	Uncertain significance (Nov 14, 2023)
9-33923830-T-A		not specified	Uncertain significance (Dec 20, 2023)
9-33923940-G-A		not specified	Uncertain significance (Nov 09, 2022)
9-33923944-G-A		not specified	Uncertain significance (Dec 12, 2023)
9-33923947-T-C		not specified	Uncertain significance (Apr 08, 2024)
9-33923976-C-T		not specified	Uncertain significance (Oct 25, 2024)
9-33923980-G-A		not specified	Uncertain significance (Feb 16, 2023)
9-33924211-T-C		not specified	Uncertain significance (May 24, 2024)
9-33924239-G-C		not specified	Uncertain significance (Jun 02, 2023)
9-33924250-G-A		not specified	Uncertain significance (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBAP2	protein_coding	protein_coding	ENST00000379238	28	127257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.43e-7	1.00	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.110	628	620	1.01	0.0000334	7205
Missense in Polyphen		166	181.69	0.91363		2215
Synonymous	-0.498	259	249	1.04	0.0000146	2315
Loss of Function	4.68	23	63.2	0.364	0.00000316	711

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000433	0.000432
Ashkenazi Jewish	0.00	0.00
East Asian	0.000274	0.000272
Finnish	0.000603	0.000601
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000274	0.000272
South Asian	0.000197	0.000196
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0856

Intolerance Scores

• loftool: 0.722
• rvis_EVS: -0.94
• rvis_percentile_EVS: 9.39

Haploinsufficiency Scores

• pHI: 0.397
• hipred: N
• hipred_score: 0.443
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubap2

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;cadherin binding